diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index f60257e03..6269fe644 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -138,7 +138,7 @@ Please see the [official docs](https://squidfunk.github.io/mkdocs-material/refer - Note that we have two custom admonitions: `exercise` and `result` (alias `solution`). - `!!!` does a regular admonition, `???` makes it collapsed (click to expand). -- Intendation is important! Make sure you check the rendered site, as it's easy to make a mistake. +- Indentation is important! Make sure you check the rendered site, as it's easy to make a mistake. ## Known limitations diff --git a/docs/advanced/index.md b/docs/advanced/index.md index 89e363df1..a2576c3fc 100644 --- a/docs/advanced/index.md +++ b/docs/advanced/index.md @@ -2,9 +2,10 @@ Welcome to our Nextflow workshop for intermediate and advanced users! -In this workshop, we will explore the advanced features of the Nextflow language and runtime, and learn how to use them to write efficient and scalable data-intensive workflows. We will cover topics such as parallel execution, error handling, and workflow customization. +In this workshop, we will explore the advanced features of the Nextflow language and runtime, and learn how to use them to write efficient and scalable data-intensive workflows. +We will cover topics such as parallel execution, error handling, and workflow customization. -Please note that this is not an introductory workshop, and we will assume some basic familiarity with Nextflow. +Please note that this is not an introductory workshop, and we will assume extensive familiarity with Nextflow. By the end of this workshop, you will have the skills and knowledge to create complex and powerful Nextflow pipelines for your own data analysis projects. @@ -34,9 +35,12 @@ Please note that this is **not** a beginner's workshop and familiarity with Next - Familiarity with Nextflow and Groovy - An understanding of common file formats -## Follow the training video +## Follow the training videos and get help -We run a free online training event for this course approximately every six months. Videos are streamed to YouTube and questions are handled in the nf-core Slack community. You can watch the recording of the most recent training ([September, 2023](https://nf-co.re/events/2023/training-sept-2023/)) below: +Video recordings are available for this course. +You can ask questions in the [Seqera community forum](https://community.seqera.io/). + +You can watch the recording of the most recent training ([September, 2023](https://nf-co.re/events/2023/training-sept-2023/)) below:
diff --git a/docs/basic_training/cache_and_resume.md b/docs/basic_training/cache_and_resume.md index 3d4713c08..a21903677 100644 --- a/docs/basic_training/cache_and_resume.md +++ b/docs/basic_training/cache_and_resume.md @@ -349,7 +349,7 @@ So D is matched with 'a' here, which was not the intention. That order will like ??? solution - You should see that while FOO and BAR reliably re-use their cache, FOOBAR will re-run at least a subset of its tasks due to differences in the combinations of inputs it recieves. + You should see that while FOO and BAR reliably re-use their cache, FOOBAR will re-run at least a subset of its tasks due to differences in the combinations of inputs it receives. The output will look like this: diff --git a/docs/basic_training/index.md b/docs/basic_training/index.md index bf224d32c..686a30a99 100644 --- a/docs/basic_training/index.md +++ b/docs/basic_training/index.md @@ -1,6 +1,7 @@ # Fundamentals Training -You are now on the path to writing reproducible and scalable scientific workflows using Nextflow. This guide complements the full [Nextflow documentation](https://www.nextflow.io/docs/latest) - if you ever have any doubts, please refer to that. +You are now on the path to writing reproducible and scalable scientific workflows using Nextflow. +This guide complements the full [Nextflow documentation](https://www.nextflow.io/docs/latest) - if you ever have any doubts, please refer to that. Let's get started! @@ -18,7 +19,10 @@ By the end of this course you should: ## Audience & prerequisites -Please note that this is **not** a beginner's workshop and familiarity with Nextflow, the command line, and common file formats is assumed. +Please note that this is **not** a beginner's workshop. +Familiarity with Nextflow, the command line, and common file formats is assumed. + +For a beginner's introduction to Nextflow, please see the [Hello Nextflow](../hello_nextflow/) course. **Prerequisites** @@ -26,9 +30,10 @@ Please note that this is **not** a beginner's workshop and familiarity with Next - Experience with command line - An understanding of common file formats -## Follow the training videos +## Follow the training videos and get help -Free online training events for this course are run approximately every six months. Videos are streamed to YouTube and questions are handled in the nf-core Slack community. +Video recordings are available for this course. +You can ask questions in the [Seqera community forum](https://community.seqera.io/). You can watch the recording of the most recent training ([March, 2024](https://nf-co.re/events/2024/training-foundational-march)) in the [YouTube playlist](https://youtu.be/dbOKB3VRpuE?si=MYBy4-gjRfEYkVRM) below: @@ -38,7 +43,7 @@ You can watch the recording of the most recent training ([March, 2024](https://n !!! warning - Please note that the training material is updated regularly and that the videos may be out of date. + Please note that the training material is updated regularly and that the videos linked below may be out of date. If English is not your preferred language, you may find it useful to follow the training from the [March 2023 event](https://nf-co.re/events/2023/training-march-2023), which is available in multiple languages. diff --git a/docs/envsetup/01_setup.md b/docs/envsetup/01_setup.md index 820689d21..c9571dc48 100644 --- a/docs/envsetup/01_setup.md +++ b/docs/envsetup/01_setup.md @@ -1,32 +1,34 @@ # Gitpod -Gitpod is a cloud development environment for teams to efficiently and securely develop software. It can improve your developer experience by coding in a cloud development environment. +Gitpod is a cloud-based development environment for teams to efficiently and securely develop software. +We use it to provide a consistent training environment for everyone. ## Creating a Gitpod account -You can create a free [Gitpod](https://gitpod.io/) account using your GitLab, GitHub, or Bitbucket account. +You can create a free [Gitpod](https://gitpod.io/) account from the [Gitpod login page](https://gitpod.io/login/). -You can create an account using the [Gitpod login page](https://gitpod.io/login/). +You will be prompted to choose between 'Gitpod Flex' and 'Gitpod Classic'. +Select 'Gitpod Classic' and click 'Continue'. -![Gitpod log in](img/login.png) - -It is best to connect your LinkedIn account to receive a full 50 hours usage allocation. +![Select 'Gitpod Classic'](img/select_gitpod_classic.png) -![Gitpod log in one step](img/onestepaway.png) +Next, log in using your GitHub account. -After selecting your preferred editor, theme, and profile details, click continue and your account will be created and ready to use. +![Gitpod log in](img/login.png) -!!! note +You may need to fill out an additional form or two. +When prompted to connect a LinkedIn account, we recommend doing so if you have one, to receive the extra 50 hours usage allocation. +Don't worry too much if you don't have one; the basic allocation is more than enough to work through the introductory training course. - It is recommended to use the VS code editor. +If you are prompted to select your preferred editor, we strongly recommend choosing the VSCode editor, as that is what we use for Nextflow development in general and for trainings in particular. ## Running Gitpod -Click the following URL to run Gitpod: +Once you are logged in to Gitpod, open this link in your browser to open the training environment: -This URL is the Nextflow training repository prefixed with `https://gitpod.io/#`. +This URL is the address to the Nextflow training repository prefixed with `https://gitpod.io/#`. -Alternatively, you can click on the button below. +Alternatively, you can click on the button shown below from the many pages in the training portal where it is displayed. [![Open Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training) @@ -34,18 +36,20 @@ If you are already logged in, your Gitpod environment will start to load. ### Explore your Gitpod IDE -After Gitpod has loaded, you should see something similar to the following: +After Gitpod has loaded, you should see something similar to the following (which may in light mode depending on your account preferences): ![Gitpod welcome](img/gitpod.welcome.png) +This is the interface of the VSCode IDE, a popular code development application that we recommend using for Nextflow development. + - **The sidebar** allows you to customize your Gitpod environment and perform basic tasks (copy, paste, open files, search, git, etc.). You can click the explorer button to see which files are in this repository. - **The terminal** allows you to run all the programs in the repository. For example, both `nextflow` and `docker` are installed and can be executed. - **The file explorer** allows you to view and edit files. Clicking on a file in the explorer will open it within the main window. -- **The Simple Browser** lets you view the nf-training material browser (). If you close it by accident, you can load the simple browser again by typing the following in the terminal: `gp preview https://training.nextflow.io`. +- **The Simple Browser** lets you view the training instructions in a web browser (). If you close it by accident, you can load the simple browser again by typing the following in the terminal: `gp preview https://training.nextflow.io`. ### Gitpod resources -Gitpod gives you 500 free credits per month, which is equivalent to 50 hours of free environment runtime using the standard workspace (up to 4 cores, 8 GB RAM, and 30 GB storage). +Gitpod gives you up to 500 free credits per month, which is equivalent to 50 hours of free environment runtime using the standard workspace (up to 4 cores, 8 GB RAM, and 30 GB storage). There is also a large workspace option that gives you up to 8 cores, 16GB RAM, and 50GB storage. However, the large workspace will use your free credits quicker and you will have fewer hours of access to this space. diff --git a/docs/envsetup/02_local.md b/docs/envsetup/02_local.md index 919d31a2d..b31b91614 100644 --- a/docs/envsetup/02_local.md +++ b/docs/envsetup/02_local.md @@ -1,6 +1,6 @@ # Local installation -If you **can not** access Gitpod you can also install everything locally. +If you **cannot** use Gitpod for any reason, you have the option of installing everything locally instead. Some requirements may be different depending on your local machine. @@ -59,7 +59,7 @@ To download the material, execute this command: git clone https://github.com/nextflow-io/training.git ``` -Then `cd` into the `nf-training` directory. +Then `cd` into the relevant directory. By default, that is `hello-nextflow`. ## Checking your installation @@ -79,7 +79,7 @@ This should print the current version, system, and runtime. nextflow info ``` - This should come up with the Nextflow version and runtime information: + This should come up with the Nextflow version and runtime information (actual versions may differ): ```console Version: 23.10.1 build 5891 diff --git a/docs/envsetup/img/gitpod.welcome.png b/docs/envsetup/img/gitpod.welcome.png index d5d4827a4..b95fff44d 100644 Binary files a/docs/envsetup/img/gitpod.welcome.png and b/docs/envsetup/img/gitpod.welcome.png differ diff --git a/docs/envsetup/img/login.png b/docs/envsetup/img/login.png index 45501c87d..ca2a05a0a 100644 Binary files a/docs/envsetup/img/login.png and b/docs/envsetup/img/login.png differ diff --git a/docs/envsetup/img/onestepaway.png b/docs/envsetup/img/onestepaway.png deleted file mode 100644 index 2280b2c18..000000000 Binary files a/docs/envsetup/img/onestepaway.png and /dev/null differ diff --git a/docs/envsetup/img/select_gitpod_classic.png b/docs/envsetup/img/select_gitpod_classic.png new file mode 100644 index 000000000..90ca641a0 Binary files /dev/null and b/docs/envsetup/img/select_gitpod_classic.png differ diff --git a/docs/hello_nextflow/01_orientation.md b/docs/hello_nextflow/00_orientation.md similarity index 53% rename from docs/hello_nextflow/01_orientation.md rename to docs/hello_nextflow/00_orientation.md index 99e3dfff7..671b467e2 100644 --- a/docs/hello_nextflow/01_orientation.md +++ b/docs/hello_nextflow/00_orientation.md @@ -1,16 +1,16 @@ # Orientation -The Gitpod environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. +The training environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface. If you have not yet done so, please follow [this link](../../envsetup/) before going any further. ## Materials provided -Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the Gitpod workspace. +Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the training workspace. This directory contains all the code files, test data and accessory files you will need. -Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the Gitpod workspace. +Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the training workspace. Alternatively, you can use the `tree` command. Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity. @@ -24,64 +24,36 @@ If you run this inside `hello-nextflow`, you should see the following output: ```console title="Directory contents" . -├── containers -│ ├── build -│ ├── data -│ ├── results -│ └── scripts -├── data -│ ├── bam -│ ├── greetings.csv -│ ├── ref -│ ├── sample_bams.txt -│ └── samplesheet.csv -├── hello-config -│ ├── demo-params.json -│ ├── main.nf -│ └── nextflow.config +├── greetings.csv +├── hello-channels.nf +├── hello-config.nf ├── hello-containers.nf -├── hello-genomics.nf -├── hello-modules -│ ├── demo-params.json -│ ├── main.nf -│ └── nextflow.config -├── hello-nf-core -│ ├── data -│ └── solution -├── hello-nf-test -│ ├── demo-params.json -│ ├── main.nf -│ ├── modules -│ └── nextflow.config -├── hello-operators.nf +├── hello-modules.nf +├── hello-workflow.nf ├── hello-world.nf ├── nextflow.config -└── solutions - ├── hello-config - ├── hello-genomics - ├── hello-modules - ├── hello-nf-test - ├── hello-operators - └── hello-world - -18 directories, 17 files +├── solutions +│ ├── 1-hello-world +│ ├── 2-hello-channels +│ ├── 3-hello-workflow +│ ├── 4-hello-modules +│ ├── 5-hello-containers +│ └── 6-hello-config +└── test-params.json + +7 directories, 9 files ``` -!!!note - - Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course. - This is just meant to give you an overview. - **Here's a summary of what you should know to get started:** - **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in. -- **The `hello-*` directories** are directories used in the later Parts of the course where we are working with more than just one workflow file. - - **The file `nextflow.config`** is a configuration file that sets minimal environment properties. You can ignore it for now. -- **The `data` directory** contains the input data we'll use in most of the course. The dataset is described in detail in Part 3, when we introduce it for the first time. +- **The file `greetings.csv`** contains input data we'll use in most of the course. It is described in Part 1, when we introduce it for the first time. + +- **The file `test-params.json`** is a file we'll use in Part 6. You can ignore it for now. - **The `solutions` directory** contains the completed workflow scripts that result from each step of the course. They are intended to be used as a reference to check your work and troubleshoot any issues. @@ -90,7 +62,7 @@ If you run this inside `hello-nextflow`, you should see the following output: !!!tip - If for whatever reason you move out of this directory, you can always run this command to return to it: + If for whatever reason you move out of this directory, you can always run this command to return to it (within the training environment): ```bash cd /workspace/gitpod/hello-nextflow diff --git a/docs/hello_nextflow/01_orientation.pt.md b/docs/hello_nextflow/00_orientation.pt.md similarity index 100% rename from docs/hello_nextflow/01_orientation.pt.md rename to docs/hello_nextflow/00_orientation.pt.md diff --git a/docs/hello_nextflow/01_hello_world.md b/docs/hello_nextflow/01_hello_world.md new file mode 100644 index 000000000..634f98936 --- /dev/null +++ b/docs/hello_nextflow/01_hello_world.md @@ -0,0 +1,686 @@ +# Part 1: Hello World + +In this first part of the Hello Nextflow training course, we ease into the topic with a very basic domain-agnostic Hello World example, which we'll progressively build up to demonstrate the usage of foundational Nextflow logic and components. + +!!! note + + A "Hello World!" is a minimalist example that is meant to demonstrate the basic syntax and structure of a programming language or software framework. The example typically consists of printing the phrase "Hello, World!" to the output device, such as the console or terminal, or writing it to a file. + +--- + +## 0. Warmup: Run Hello World directly + +Let's demonstrate this with a simple command that we run directly in the terminal, to show what it does before we wrap it in Nextflow. + +### 0.1. Make the terminal say hello + +```bash +echo 'Hello World!' +``` + +This outputs the text 'Hello World' to the terminal. + +```console title="Output" +Hello World! +``` + +### 0.2. Now make it write the text output to a file + +```bash +echo 'Hello World!' > output.txt +``` + +This does not output anything to the terminal. + +```console title="Output" + +``` + +### 0.3. Show the file contents + +```bash +cat output.txt +``` + +The text 'Hello World' is now in the output file we specified. + +```console title="output.txt" linenums="1" +Hello World! +``` + +!!! tip + + In the training environment, you can also find the output file in the file explorer, and view its contents by clicking on it. Alternatively, you can use the `code` command to open the file for viewing. + + ```bash + code output.txt + ``` + +### Takeaway + +You now know how to run a simple command in the terminal that outputs some text, and optionally, how to make it write the output to a file. + +### What's next? + +Find out what that would look like written as a Nextflow workflow. + +--- + +## 1. Examine the Hello World workflow starter script + +As mentioned in the orientation, we provide you with a fully functional if minimalist workflow script named `hello-world.nf` that does the same thing as before (write out 'Hello World!') but with Nextflow. + +To get you started, we'll first open up the workflow script so you can get a sense of how it's structured. + +### 1.1. Examine the overall code structure + +Let's open the `hello-world.nf` script in the editor pane. + +!!! note + + The file is in the `hello-nextflow` directory, which should be your current working directory. + You can either click on the file in the file explorer, or type `ls` in the terminal and Cmd+Click (MacOS) or Ctrl+Click (PC) on the file to open it. + +```groovy title="hello-world.nf" linenums="1" +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + output: + path 'output.txt' + + script: + """ + echo 'Hello World!' > output.txt + """ +} + +workflow { + + // emit a greeting + sayHello() +} +``` + +As you can see, a Nextflow script involves two main types of core components: one or more **processes**, and the **workflow** itself. +Each **process** describes what operation(s) the corresponding step in the pipeline should accomplish, while the **workflow** describes the dataflow logic that connects the various steps. + +Let's take a closer look at the **process** block first, then we'll look at the **workflow** block. + +### 1.2 The `process` definition + +The first block of code describes a **process**. +The process definition starts with the keyword `process`, followed by the process name and finally the process body delimited by curly braces. +The process body must contain a script block which specifies the command to run, which can be anything you would be able to run in a command line terminal. + +Here we have a **process** called `sayHello` that writes its **output** to a file named `output.txt`. + +```groovy title="hello-world.nf" linenums="3" +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + output: + path 'output.txt' + + script: + """ + echo 'Hello World!' > output.txt + """ +} +``` + +This a very minimal process definition that just contains an `output` definition and the `script` to execute. + +The `output` definition includes the `path` qualifier, which tells Nextflow this should be handled as a path (includes both directory paths and files). +Another common qualifier is `val`. + +!!! note + + The output definition does not _determine_ what output will be created. + It simply _declares_ what is the expected output, so that Nextflow can look for it once execution is complete. + This is necessary for verifying that the command was executed successfully and for passing the output to downstream processes if needed. + +!!! warning + + This example is brittle because we hardcoded the output filename in two separate places (the script and the output blocks). + If we change one but not the other, the script will break. + Later, you'll learn how to use variables to avoid this problem. + +In a real-world pipeline, a process usually contains additional blocks such as directives, inputs, and conditional clauses, which we'll introduce later in this training course. + +### 1.3 The `workflow` definition + +The second block of code describes the **workflow** itself. +The workflow definition starts with the keyword `workflow`, followed by an optional name, then the workflow body delimited by curly braces. + +Here we have a **workflow** that consists of one call to the `sayHello` process. + +```groovy title="hello-world.nf" linenums="17" +workflow { + + // emit a greeting + sayHello() +} +``` + +This a very minimal **workflow** definition. +In a real-world pipeline, the workflow typically contains multiple calls to **processes** connected by **channels**, and the processes expect one or more variable **input(s)**. + +You'll learn how to add variable inputs later in this training module; and you'll learn how to add more processes and connect them by channels in Part 3 of this course. + +### Takeaway + +You now know how a simple Nextflow workflow is structured. + +### What's next? + +Learn to launch the workflow, monitor execution and find your outputs. + +--- + +## 2. Run the workflow + +Looking at code is not nearly as fun as running it, so let's try this out in practice. + +### 2.1. Launch the workflow and monitor execution + +In the terminal, run the following command: + +```bash +nextflow run hello-world.nf +``` + +You console output should look something like this: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-world.nf` [goofy_torvalds] DSL2 - revision: c33d41f479 + +executor > local (1) +[a3/7be2fa] sayHello | 1 of 1 ✔ +``` + +Congratulations, you just ran your first Nextflow workflow! + +The most important output here is the last line (line 6): + +```console title="Output" linenums="6" +[a3/7be2fa] sayHello | 1 of 1 ✔ +``` + +This tells us that the `sayHello` process was successfully executed once (`1 of 1 ✔`). + +Importantly, this line also tells you where to find the output of the `sayHello` process call. +Let's look at that now. + +### 2.2. Find the output and logs in the `work` directory + +When you run Nextflow for the first time in a given directory, it creates a directory called `work` where it will write all files (and any symlinks) generated in the course of execution. + +Within the `work` directory, Nextflow organizes outputs and logs per process call. +For each process call, Nextflow creates a nested subdirectory, named with a hash in order to make it unique, where it will stage all necessary inputs (using symlinks by default), write helper files, and write out logs and any outputs of the process. + +The path to that subdirectory is shown in truncated form in square brackets in the console output. +Looking at what we got for the run shown above, the console log line for the sayHello process starts with `[a3/7be2fa]`. That corresponds to the following directory path: `work/`**`a3/7be2fa`**`7be2fad5e71e5f49998f795677fd68` + +Let's take a look at what's in there. + +!!! tip + + If you browse the contents of the task subdirectory in the VSCode file explorer, you'll see all the files right away. + However, the log files are set to be invisible in the terminal, so if you want to use `ls` or `tree` to view them, you'll need to set the relevant option for displaying invisible files. + + ```bash + tree -a work + ``` + +You should see something like this, though the exact subdirectory names will be different on your system: + +```console title="Directory contents" +work +└── a3 + └── 7be2fad5e71e5f49998f795677fd68 + ├── .command.begin + ├── .command.err + ├── .command.log + ├── .command.out + ├── .command.run + ├── .command.sh + ├── .exitcode + └── output.txt +``` + +These are the helper and log files: + +- **`.command.begin`**: Metadata related to the beginning of the execution of the process call +- **`.command.err`**: Error messages (`stderr`) emitted by the process call +- **`.command.log`**: Complete log output emitted by the process call +- **`.command.out`**: Regular output (`stdout`) by the process call +- **`.command.run`**: Full script run by Nextflow to execute the process call +- **`.command.sh`**: The command that was run by the process call call +- **`.exitcode`**: The exit code resulting from the command + +The `.command.sh` file is especially useful because it tells you what command Nextflow actually executed. +In this case it's very straightforward, but later in the course you'll see commands that involve some interpolation of variables. +When you're dealing with that, you need to be able to check exactly what was run, especially when troubleshooting an issue. + +The actual output of the `sayHello` process is `output.txt`. +Open it and you will find the `Hello World!` greeting, which was the expected result of our minimalist workflow. + +```console title="output.txt" linenums="1" +Hello World! +``` + +### Takeaway + +You know how to decipher a simple Nextflow script, run it and find the output and relevant log files in the work directory. + +### What's next? + +Learn how to manage your workflow executions conveniently. + +--- + +## 3. Manage workflow executions + +Knowing how to launch workflows and retrieve outputs is great, but you'll quickly find there are a few other aspects of workflow management that will make your life easier, especially if you're developing your own workflows. + +Here we show you how to use the `publishDir` directive to TODO, the `resume` feature for when you need to re-launch the same workflow, and how to delete older work directories with `nextflow clean`. + +### 3.1. Publish outputs + +As you have just learned, the output produced by our pipeline is buried in a working directory several layers deep. +This is done on purpose; Nextflow is in control of this directory and we are not supposed to interact with it. + +However, that makes it inconvenient to retrieve outputs that we care about. + +Fortunately, Nextflow provides a way to manage this more conveniently, called the `publishDir` directive, which acts at the process level. +This directive tells Nextflow to copy the output(s) of the process to a designated output directory. +It allows us to retrieve the desired output file without having to dig down into the work directory. + +#### 3.1.1. Add a `publishDir` directive to the `sayHello` process + +In the workflow script file `hello-world.nf`, make the following code modification: + +_Before:_ + +```groovy title="hello-world.nf" linenums="6" +process sayHello { + + output: + path 'output.txt' +``` + +_After:_ + +```groovy title="hello-world.nf" linenums="6" +process sayHello { + + publishDir 'results', mode: 'copy' + + output: + path 'output.txt' +``` + +#### 3.1.2. Run the workflow again + +Now run the modified workflow script: + +```bash +nextflow run hello-world.nf +``` + +The log output should look very familiar: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-world.nf` [jovial_mayer] DSL2 - revision: 35bd3425e5 + +executor > local (1) +[62/49a1f8] sayHello | 1 of 1 ✔ +``` + +This time, Nextflow has created a new directory called `results/`. +Our `output.txt` file is in this directory. +If you check the contents it should match the output in the work subdirectory. +This is how we move results files outside of the working directories conveniently. + +It is also possible to set the `publishDir` directive to make a symbolic link to the file instead of actually copying it. +This is preferable when you're dealing with very large files you don't need to retain longer term. +However, if you delete the work directory as part of a cleanup operation, you will lost access to the file, so always make sure you have actual copies of everything you care about before deleting anything. + +!!! note + + A newer syntax option had been proposed to make it possible to declare and publish workflow-level outputs, documented [here](https://www.nextflow.io/docs/latest/workflow.html#publishing-outputs). + This will eventually make using `publishDir` at the process level redundant for completed pipelines. + However, we expect that `publishDir` will still remain very useful during pipeline development. + +### 3.2. Re-launch a workflow with `-resume` + +Sometimes, you're going to want to re-run a pipeline that you've already launched previously without redoing any steps that already completed successfully. + +Nextflow has an option called `-resume` that allows you to do this. +Specifically, in this mode, any processes that have already been run with the exact same code, settings and inputs will be skipped. +This means Nextflow will only run processes that you've added or modified since the last run, or to which you're providing new settings or inputs. + +There are two key advantages to doing this: + +- If you're in the middle of developing your pipeline, you can iterate more rapidly since you only have to run the process(es) you're actively working on in order to test your changes. +- If you're running a pipeline in production and something goes wrong, in many cases you can fix the issue and relaunch the pipeline, and it will resume running from the point of failure, which can save you a lot of time and compute. + +To use it, simply add `-resume` to your command and run it: + +```bash +nextflow run hello-world.nf -resume +``` + +The console output should look similar. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-world.nf` [golden_cantor] DSL2 - revision: 35bd3425e5 + +[62/49a1f8] sayHello | 1 of 1, cached: 1 ✔ +``` + +Look for the `cached:` bit that has been added in the process status line (line 6), which means that Nextflow has recognized that it has already done this work and simply re-used the result from the previous successful run. + +You can also see that the work subdirectory hash is the same as in the previous run. +Nextflow is literally pointing you to the previous execution and saying "I already did that over there." + +!!! note + + When your re-run a pipeline with `resume`, Nextflow does not overwrite any files written to a `publishDir` directory by any process call that was previously run successfully. + +### 3.3. Delete older work directories + +During the development process, you'll typically run your draft pipelines a large number of times, which can lead to an accumulation of very many files across many subdirectories. +Since the subdirectories are named randomly, it is difficult to tell from their names what are older vs. more recent runs. + +Nextflow includes a convenient `-clean` command that can automatically delete the work subdirectories for past runs that you no longer care about, with several [options](https://www.nextflow.io/docs/latest/reference/cli.html#clean) to control what will be deleted. + +Here we show you an example that deletes all subdirectories from runs before a given run, specified using its run name. +The run name is the machine-generated two-part string shown in square brackets in the `Launching (...)` console output line. + +First we use the dry run flag `-n` to check what will be deleted given the command: + +```bash +nextflow clean -before golden_cantor -n +``` + +The output should look like this: + +```console title="Output" +Would remove /workspace/gitpod/hello-nextflow/work/a3/7be2fad5e71e5f49998f795677fd68 +``` + +If you don't see any lines output, you either did not provide a valid run name or there are no past runs to delete. + +If the output looks as expected and you want to proceed with the deletion, re-run the command with the `-f` flag instead of `-n`: + +```bash +nextflow clean -before golden_cantor -f +``` + +You should now see the following: + +```console title="Output" +Removed /workspace/gitpod/hello-nextflow/work/a3/7be2fad5e71e5f49998f795677fd68 +``` + +!!! Warning + + Deleting work subdirectories from past runs removes them from Nextflow's cache and deletes any outputs that were stored in those directories. + That means it breaks Nextflow's ability to resume execution without re-running the corresponding processes. + + You are responsible for saving any outputs that you care about or plan to rely on! If you're using the `publishDir` directive for that purpose, make sure to use the `copy` mode, not the `symlink` mode. + +### Takeaway + +You know how to publish outputs to a specific directory, relaunch a pipeline without repeating steps that were already run in an identical way, and use the `nextflow clean` command to clean up old work directories. + +### What's next? + +Learn to provide a variable input via a command-line parameter and utilize default values effectively. + +--- + +## 4. Use a variable input passed on the command line + +In its current state, our workflow uses a greeting hardcoded into the process command. +We want to add some flexibility by using an input variable, so that we can more easily change the greeting at runtime. + +### 4.1. Modify the workflow to take and use a variable input + +This requires us to make three changes to our script: + +1. Tell the process to expect a variable input by adding an `input:` block +2. Edit the process to use the input +3. Set up a command-line parameter and provide its value as an input to the process call + +Let's make these changes one at a time. + +#### 4.1.1. Add an input block to the process definition + +First we need to adapt the process definition to accept an input called `greeting`. + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="6" +process sayHello { + + publishDir 'results', mode: 'copy' + + output: + path 'output.txt' +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="6" +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path 'output.txt' +``` + +The `greeting` variable is prefixed by `val` to tell Nextflow it's a value (not a path). + +#### 4.1.2. Edit the process command to use the input variable + +Now we swap the original hardcoded value for the value of the input variable we expect to receive. + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="16" +script: +""" +echo 'Hello World!' > output.txt +""" +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="16" +script: +""" +echo '$greeting' > output.txt +""" +``` + +Make sure to prepend the `$` symbol to tell Nextflow this is a variable name that needs to be replaced with the actual value (=interpolated). + +#### 4.1.3. Set up a CLI parameter and provide it as input to the process call + +Now we need to actually set up a way to provide an input value to the `sayHello()` process call. + +We could simply hardcode it directly by writing `sayHello('Hello World!')`. +However, when we're doing real work with our workflow, we're often going to want to be able to control its inputs from the command line. + +Good news: Nextflow has a built-in workflow parameter system called `params`, which makes it easy to declare and use CLI parameters. The general syntax is to declare `params.` to tell Nextflow to expect a `--` parameter on the command line. + +Here, we want to create a parameter called `--greeting`, so we need to declare `params.greeting` somewhere in the workflow. +In principle we can write it anywhere; but since we're going to want to give it to the `sayHello()` process call, we can plug it in there directly by writing `sayHello(params.greeting)`. + +!!! note + + The parameter name (at the workflow level) does not have to match the input variable name (at the process level). + We're just using the same word because that's what makes sense and keeps the code readable. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-world.nf" linenums="24" +// emit a greeting +sayHello() +``` + +_After:_ + +```groovy title="hello-world.nf" linenums="24" +// emit a greeting +sayHello(params.greeting) +``` + +This tells Nextflow to run the `sayHello` process on the value provided through the `--greeting` parameter. + +#### 4.1.4. Run the workflow command again + +Let's run it! + +```bash +nextflow run hello-world.nf --greeting 'Bonjour le monde!' +``` + +If you made all three edits correctly, you should get another successful execution: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-world.nf` [elated_lavoisier] DSL2 - revision: 7c031b42ea + +executor > local (1) +[4b/654319] sayHello | 1 of 1 ✔ +``` + +Be sure to open up the output file to check that you now have the new version of the greeting. + +```console title="output.txt" linenums="1" +Bonjour le monde! +``` + +Voilà! + +!!! tip + + You can readily distinguish Nextflow-level parameters from pipeline-level parameters. + + - Parameters that apply to a pipeline always take a double hyphen (`--`). + - Parameters that modify a Nextflow setting, _e.g._ the `-resume` feature we used earlier, take a single hyphen (`-`). + +### 4.2. Use default values for command line parameters + +In many cases, it makes sense to supply a default value for a given parameter so that you don't have to specify it for every run. + +#### 4.2.1. Set a default value for the CLI parameter + +Let's give the `greeting` parameter with a default value by declaring it before the workflow definition. + +```groovy title="hello-world.nf" linenums="22" +/* + * Pipeline parameters + */ +params.greeting = 'Holà mundo!' +``` + +!!! tip + + You can put the parameter declaration inside the workflow block if you prefer. Whatever you choose, try to group similar things in the same place so you don't end up with declarations all over the place. + +#### 4.2.2. Run the workflow again without specifying the parameter + +Now that you have a default value set, you can run the workflow again without having to specify a value in the command line. + +```bash +nextflow run hello-world.nf +``` + +The console output should look the same. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-world.nf` [determined_edison] DSL2 - revision: 3539118582 + +executor > local (1) +[72/394147] sayHello | 1 of 1 ✔ +``` + +Check the output in the results directory: + +```console title="output.txt" linenums="1" +Holà mundo! +``` + +Nextflow used the default value to name the output. + +#### 4.2.3. Run the workflow again with the parameter to override the default value + +If you provide the parameter on the command line, the CLI value will override the default value. + +Try it out: + +```bash +nextflow run hello-world.nf --greeting 'Konnichiwa!' +``` + +The console output should look the same. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-world.nf` [elegant_faraday] DSL2 - revision: 3539118582 + +executor > local (1) +[6f/a12a91] sayHello | 1 of 1 ✔ +``` + +Now you will have the corresponding new output in your results directory. + +```console title="output.txt" linenums="1" +Konnichiwa! +``` + +!!! note + + In Nextflow, there are multiple places where you can specify values for parameters. + If the same parameter is set to different values in multiple places, Nexflow will determine what value to use based on the order of precedence that is described [here](https://www.nextflow.io/docs/latest/config.html). + +### Takeaway + +You know how to use a simple variable input provided at runtime via a command-line parameter, as well as set up, use and override default values. + +More generally, you know how to interpret a simple Nextflow workflow, manage its execution, and retrieve outputs. + +### What's next? + +Take a little break, you've earned it! +When you're ready, move on to Part 2 to learn how to use channels to feed inputs into your workflow, which will allow you to take advantage of Nextflow's built-in dataflow parallelism and other powerful features. diff --git a/docs/hello_nextflow/02_hello_channels.md b/docs/hello_nextflow/02_hello_channels.md new file mode 100644 index 000000000..54eba99d7 --- /dev/null +++ b/docs/hello_nextflow/02_hello_channels.md @@ -0,0 +1,880 @@ +# Part 2: Hello Channels + +In Part 1 of this course (Hello World), we showed you how to provide a variable input to a process by providing the input in the process call directly: `sayHello(params.greet)`. +That was a deliberately simplified approach. +In practice, that approach has major limitations; namely that it only works for very simple cases where we only want to run the process once, on a single value. +In most realistic workflow use cases, we want to process multiple values (experimental data for multiple samples, for example), so we need a more sophisticated way to handle inputs. + +That is what Nextflow **channels** are for. +Channels are queues designed to handle inputs efficiently and shuttle them from one step to another in multi-step workflows, while providing built-in parallelism and many additional benefits. + +In this part of the course, you will learn how to use a channel to handle multiple inputs from a variety of different sources. +You will also learn to use **operators** to transform channel contents as needed. + +_For training on using channels to connect steps in a multi-step workflow, see Part 3 of this course._ + +--- + +## 0. Warmup: Run `hello-channels.nf` + +We're going to use the workflow script `hello-channels.nf` as a starting point. +It is equivalent to the script produced by working through Part 1 of this training course. + +Just to make sure everything is working, run the script once before making any changes: + +```bash +nextflow run hello-channels.nf --greeting 'Hello Channels!' +``` + +```console title="Output" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [insane_lichterman] DSL2 - revision: c33d41f479 + +executor > local (1) +[86/9efa08] sayHello | 1 of 1 ✔ +``` + +As previously, you will find the output file named `output.txt` in the `results` directory (specified by the `publishDir` directive). + +```console title="output.txt" linenums="1" +Hello Channels! +``` + +If that worked for you, you're ready to learn about channels. + +--- + +## 1. Provide variable inputs via a channel explicitly + +We are going to create a **channel** to pass the variable input to the `sayHello()` process instead of relying on the implicit handling, which has certain limitations. + +### 1.1. Create an input channel + +There are a variety of **channel factories** that we can use to set up a channel. +To keep things simple for now, we are going to use the most basic channel factory, called `Channel.of`, which will create a channel containing a single value. +Functionally this will be exactly equivalent to how we had it set up before, but explicit instead of implicit. + +This is the line of code we're going to use: + +```console title="Syntax" +greeting_ch = Channel.of('Hello Channels!') +``` + +This creates a channel called `greeting_ch` using the `Channel.of()` channel factory, which sets up a simple value channel, and loads the string `'Hello Channels!'` to use as the greeting value. + +!!! note + + We are temporarily switching back to hardcoded strings instead of using a CLI parameter for the sake of readability. We'll go back to using CLI parameters once we've covered what's happening at the level of the channel. + +In the workflow block, add the channel factory code: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="27" +workflow { + + // emit a greeting + sayHello(params.greeting) +} +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="27" +workflow { + + // create a channel for inputs + greeting_ch = Channel.of('Hello Channels!') + + // emit a greeting + sayHello(params.greeting) +} +``` + +This is not yet functional since we haven't yet switched the input to the process call. + +### 1.2. Add the channel as input to the process call + +Now we need to actually plug our newly created channel into the `sayHello()` process call, replacing the CLI parameter which we were providing directly before. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="27" +workflow { + + // create a channel for inputs + greeting_ch = Channel.of('Hello Channels!') + + // emit a greeting + sayHello(params.greeting) +} +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="27" +workflow { + + // create a channel for inputs + greeting_ch = Channel.of('Hello Channels!') + + // emit a greeting + sayHello(greeting_ch) +} +``` + +This tells Nextflow to run the `sayHello` process on the contents of the `greeting_ch` channel. + +Now our workflow is properly functional; it is the explicit equivalent of writing `sayHello('Hello Channels!')`. + +### 1.3. Run the workflow command again + +Let's run it! + +```bash +nextflow run hello-channels.nf +``` + +If you made both edits correctly, you should get another successful execution: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [nice_heisenberg] DSL2 - revision: 41b4aeb7e9 + +executor > local (1) +[3b/f2b109] sayHello (1) | 1 of 1 ✔ +``` + +You can check the results directory to satisfy yourself that the outcome is still the same as previously. + +```console title="output.txt" linenums="1" +Hello Channels! +``` + +So far we're just progressively tweaking the code to increase the flexibility of our workflow while achieving the same end result. + +!!! note + + This may seem like we're writing more code for no tangible benefit, but the value will become clear as soon as we start handling more inputs. + +### Takeaway + +You know how to use a basic channel factory to provide an input to a process. + +### What's next? + +Learn how to use channels to make the workflow iterate over multiple input values. + +--- + +## 2. Modify the workflow to run on multiple input values + +Workflows typically run on batches of inputs that are meant to be processed in bulk, so we want to upgrade the workflow to accept multiple input values. + +### 2.1. Load multiple greetings into the input channel + +Conveniently, the `Channel.of()` channel factory we've been using is quite happy to accept more than one value, so we don't need to modify that at all. +We just have to load more values into the channel. + +#### 2.1.1. Add more greetings + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="29" +// create a channel for inputs +greeting_ch = Channel.of('Hello Channels') +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="29" +// create a channel for inputs +greeting_ch = Channel.of('Hello','Bonjour','Holà') +``` + +The documentation tells us this should work. Can it really be so simple? + +#### 2.1.2. Run the command and look at the log output + +Let's try it. + +```bash +nextflow run hello-channels.nf +``` + +It certainly seems to run just fine: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [suspicious_lamport] DSL2 - revision: 778deadaea + +executor > local (3) +[cd/77a81f] sayHello (3) | 3 of 3 ✔ +``` + +However... This seems to indicate that '3 of 3' calls were made for the process, which is encouraging, but this only shows us a single run of the process, with one subdirectory path (`cd/77a81f`). +What's going on? + +By default, the ANSI logging system writes the logging from multiple calls to the same process on the same line. +Fortunately, we can disable that behavior to see the full list of process calls. + +#### 2.1.3. Run the command again with the `-ansi-log false` option + +To expand the logging to display one line per process call, add `-ansi-log false` to the command. + +```bash +nextflow run hello-channels.nf -ansi-log false +``` + +This time we see all three process runs and their associated work subdirectories listed in the output: + +```console title="Output" linenums="1" +N E X T F L O W ~ version 24.10.0 +Launching `hello-channels.nf` [pensive_poitras] DSL2 - revision: 778deadaea +[76/f61695] Submitted process > sayHello (1) +[6e/d12e35] Submitted process > sayHello (3) +[c1/097679] Submitted process > sayHello (2) +``` + +That's much better; at least for a simple workflow. +For a complex workflow, or a large number of inputs, having the full list output to the terminal might get a bit overwhelming, so you might not choose to use `-ansi-log false` in those cases. + +!!! note + + The way the status is reported is a bit different between the two logging modes. + In the condensed mode, Nextflow reports whether calls were completed successfully or not. + In this expanded mode, it only reports that they were submitted. + +That being said, we have another problem. If you look in the `results` directory, there is only one file: `output.txt`! + +```console title="Directory contents" +results +└── output.txt +``` + +What's up with that? Shouldn't we be expecting a separate file per input greeting, so three files in all? +Did all three greetings go into a single file? + +You can check the contents of `output.txt`; you will find only one of the three, containing one of the three greetings we provided. + +```console title="output.txt" linenums="1" +Bonjour +``` + +You may recall that we hardcoded the output file name for the `sayHello` process, so all three calls produced a file called `output.txt`. +You can check the work subdirectories for each of the three processes; each of them contains a file called `output.txt` as expected. + +As long as the output files stay there, isolated from the other processes, that is okay. +But when the `publishDir` directive copies each of them to the same `results` directory, whichever got copied there first gets overwritten by the next one, and so on. + +### 2.2. Ensure the output file names will be unique + +We can continue publishing all the outputs to the same results directory, but we need to ensure they will have unique names. +Specifically, we need to modify the first process to generate a file name dynamically so that the final file names will be unique. + +So how do we make the file names unique? +A common way to do that is to use some unique piece of metadata from the inputs (received from the input channel) as part of the output file name. +Here, for convenience, we'll just use the greeting itself since it's just a short string, and prepend it to the base output filename. + +#### 2.2.1. Construct a dynamic output file name + +In the process block, make the following code changes: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="6" +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path 'output.txt' + + script: + """ + echo '$greeting' > output.txt + """ +} +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="6" +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} +``` + +Make sure to replace `output.txt` in both the output definition and in the `script:` command block. + +!!! tip + + In the output definition, you MUST use double quotes around the output filename expression (NOT single quotes), otherwise it will fail. + +This should produce a unique output file name every time the process is called, so that it can be distinguished from the outputs from other iterations of the same process in the output directory. + +#### 2.2.2. Run the workflow + +Let's run it: + +```bash +nextflow run hello-channels.nf +``` + +Reverting back to the summary view, the output looks like this again: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [astonishing_bell] DSL2 - revision: f57ff44a69 + +executor > local (3) +[2d/90a2e2] sayHello (1) | 3 of 3 ✔ +``` + +Importantly, now we have three new files in addition to the one we already had in the `results` directory: + +```console title="Directory contents" +results +├── Bonjour-output.txt +├── Hello-output.txt +├── Holà-output.txt +└── output.txt +``` + +They each have the expected contents: + +```console title="Bonjour-output.txt" linenums="1" +Bonjour +``` + +```console title="Hello-output.txt" linenums="1" +Hello +``` + +```console title="Holà-output.txt" linenums="1" +Holà +``` + +Success! Now we can add as many greetings as we like without worrying about output files being overwritten. + +!!! note + + In practice, naming files based on the input data itself is almost always impractical. + The better way to generate dynamic filenames is to pass metadata to a process along with the input files. + The metadata is typically provided via a 'sample sheet' or equivalents. + You'll learn how to do that later in your Nextflow training. + +### Takeaway + +You know how to feed multiple input elements through a channel. + +### What's next? + +Learn to use an operator to transform the contents of a channel. + +--- + +## 3. Use an operator to transform the contents of a channel + +In Nextflow, [operators](https://www.nextflow.io/docs/latest/reference/operator.html) allow us to transform the contents of a channel. + +We just showed you how to handle multiple input elements that were hardcoded directly in the channel factory. +What if we wanted to provide those multiple inputs in a different form? + +For example, imagine we set up an input variable containing an array of elements like this: + +`greetings_array = ['Hello','Bonjour','Holà']` + +Can we load that into our output channel and expect it to work? Let's find out. + +### 3.1. Provide an array of values as input to the channel + +Common sense suggests we should be able to simply pass in an array of values instead of a single value. Right? + +#### 3.1.1. Set up the input variable + +Let's take the `greetings_array` variable we just imagined and make it a reality by adding it to the workflow block: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="27" +workflow { + + // create a channel for inputs + greeting_ch = Channel.of('Hello','Bonjour','Holà') +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="27" +workflow { + + // declare an array of input greetings + greetings_array = ['Hello','Bonjour','Holà'] + + // create a channel for inputs + greeting_ch = Channel.of('Hello','Bonjour','Holà') +``` + +#### 3.1.2. Set array of greetings as the input to the channel factory + +We're going to replace the values `'Hello','Bonjour','Holà'` currently hardcoded in the channel factory with the `greetings_array` we just created. + +In the workflow block, make the following change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="32" + // create a channel for inputs + greeting_ch = Channel.of('Hello','Bonjour','Holà') +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="32" + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) +``` + +#### 3.1.3. Run the workflow + +Let's try running this: + +```bash +nextflow run hello-channels.nf +``` + +Oh no! Nextflow throws an error that starts like this: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [friendly_koch] DSL2 - revision: 97256837a7 + +executor > local (1) +[22/57e015] sayHello (1) | 0 of 1 +ERROR ~ Error executing process > 'sayHello (1)' + +Caused by: + Missing output file(s) `[Hello, Bonjour, Holà]-output.txt` expected by process `sayHello (1)` +``` + +It looks like Nextflow tried to run a single process call, using `[Hello, Bonjour, Holà]` as a string value, instead of using the three strings in the array as separate values. + +How do we get Nextflow to unpack the array and load the individual strings into the channel? + +### 3.2. Use an operator to transform channel contents + +This is where **operators** come in. + +If you skim through the [list of operators](https://www.nextflow.io/docs/latest/reference/operator.html) in the Nextflow documentation, you'll find [`flatten()`](https://www.nextflow.io/docs/latest/reference/operator.html#flatten), which does exactly what we need: unpack the contents of an array and emits them as individual items. + +!!! note + + It is technically possible to achieve the same results by using a different channel factory, [`Channel.fromList`](https://nextflow.io/docs/latest/reference/channel.html#fromlist), which includes an implicit mapping step in its operation. + Here we chose not to use that in order to demonstrate the use of an operator on a fairly simple use case. + +#### 3.2.1. Add the `flatten()` operator + +To apply the `flatten()` operator to our input channel, we append it to the channel factory declaration. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="31" + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="31" + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) + .flatten() +``` + +Here we added the operator on the next line for readability, but you can add operators on the same line as the channel factory if you prefer, like this: `greeting_ch = Channel.of(greetings_array).flatten()` + +#### 3.2.2. Add `view()` to inspect channel contents + +We could run this right away to test if it works, but while we're at it, we're also going to add a couple of [`view()`](https://www.nextflow.io/docs/latest/reference/operator.html#view) directives, which allow us to inspect the contents of a channel. +You can think of `view()` as a debugging tool, like a `print()` statement in Python, or its equivalent in other languages. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="31" + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) + .flatten() +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="31" + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) + .view { "Before flatten: $it" } + .flatten() + .view { "After flatten: $it" } +``` + +Here `$it` is an implicit variable that represents each individual item loaded in a channel. + +#### 3.2.3. Run the workflow + +Finally, you can try running the workflow again! + +```bash +nextflow run hello-channels.nf +``` + +This time it works AND gives us the additional insight into what the contents of the channel look like before and after we run the `flatten()` operator: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [tiny_elion] DSL2 - revision: 1d834f23d2 + +executor > local (3) +[8e/bb08f3] sayHello (2) | 3 of 3 ✔ +Before flatten: [Hello, Bonjour, Holà] +After flatten: Hello +After flatten: Bonjour +After flatten: Holà +``` + +You see that we get a single `Before flatten:` statement because at that point the channel contains one item, the original array. +Then we get three separate `After flatten:` statements, one for each greeting, which are now individual items in the channel. + +Importantly, this means each item can now be processed separately by the workflow. + +!!! tip + + You should delete or comment out the `view()` statements before moving on. + + ```groovy title="hello-channels.nf" linenums="31" + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) + .flatten() + ``` + + We left them in the `hello-channels-3.nf` solution file for reference purposes. + +### Takeaway + +You know how to use an operator like `flatten()` to transform the contents of a channel, and how to use the `view()` directive to inspect channel contents before and after applying an operator. + +### What's next? + +Learn how to make the workflow take a file as its source of input values. + +--- + +## 4. Use an operator to parse input values from a CSV file + +It's often the case that, when we want to run on multiple inputs, the input values are contained in a file. +As an example, we prepared a CSV file called `greetings.csv` containing several greetings, one on each line (like a column of data). + +```csv title="greetings.csv" linenums="1" +Hello +Bonjour +Holà +``` + +So now we need to modify our workflow to read in the values from a file like that. + +### 4.1. Modify the script to expect a CSV file as the source of greetings + +To get started, we're going to need to make two key changes to the script: + +- Switch the input parameter to point to the CSV file +- Switch to a channel factory designed to handle a file + +#### 4.1.1. Switch the input parameter to point to the CSV file + +Remember the `params.greeting` parameter we set up in Part1? +We're going to update it to point to the CSV file containing our greetings. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="25" +/* + * Pipeline parameters + */ +params.greeting = ['Hello','Bonjour','Holà'] +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="25" +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +``` + +#### 4.1.2. Switch to a channel factory designed to handle a file + +Since we now want to use a file instead of simple values as the input, we can't use the `Channel.of()` channel factory from before. +We need to switch to using a new channel factory, [`Channel.fromPath()`](https://www.nextflow.io/docs/latest/reference/channel.html#channel-path), which has some built-in functionality for handling file paths. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="31" + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) + .flatten() +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="31" + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) +``` + +#### 4.1.3. Run the workflow + +Let's try running the workflow with the new channel factory and the input file. + +```bash +nextflow run hello-channels.nf +``` + +Oh no, it doesn't work. Here's the start of the console output and error message: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [adoring_bhabha] DSL2 - revision: 8ce25edc39 + +[- ] sayHello | 0 of 1 +ERROR ~ Error executing process > 'sayHello (1)' + +Caused by: + File `/workspace/gitpod/hello-nextflow/data/greetings.csv-output.txt` is outside the scope of the process work directory: /workspace/gitpod/hello-nextflow/work/e3/c459b3c8f4029094cc778c89a4393d + + +Command executed: + + echo '/workspace/gitpod/hello-nextflow/data/greetings.csv' > '/workspace/gitpod/hello-nextflow/data/greetings. +``` + +The `Command executed:` bit (lines 13-15) is especially helpful here. + +This may look a little bit familiar. +It looks like Nextflow tried to run a single process call using the file path itself as a string value. +So it has resolved the file path correctly, but it didn't actually parse its contents, which is what we wanted. + +How do we get Nextflow to open the file and load its contents into the channel? + +Sounds like we need another [operator](https://www.nextflow.io/docs/latest/reference/operator.html)! + +### 4.2. Use the `splitCsv()` operator to parse the file + +Looking through the list of operators again, we find [`splitCsv()`](https://www.nextflow.io/docs/latest/reference/operator.html#splitCsv), which is designed to parse and split CSV-formatted text. + +#### 4.2.1. Apply `splitCsv()` to the channel + +To apply the operator, we append it to the channel factory line like previously. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="31" +// create a channel for inputs from a CSV file +greeting_ch = Channel.fromPath(params.greeting) +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="31" +// create a channel for inputs from a CSV file +greeting_ch = Channel.fromPath(params.greeting) + .view { "Before splitCsv: $it" } + .splitCsv() + .view { "After splitCsv: $it" } +``` + +As you can see, we also include before/after view statements while we're at it. + +#### 4.2.2. Run the workflow again + +Let's try running the workflow with the added CSV-parsing logic. + +```bash +nextflow run hello-channels.nf +``` + +Interestingly, this fails too, but with a different error. The console output and error starts like this: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [stoic_ride] DSL2 - revision: a0e5de507e + +executor > local (3) +[42/8fea64] sayHello (1) | 0 of 3 +Before splitCsv: /workspace/gitpod/hello-nextflow/greetings.csv +After splitCsv: [Hello] +After splitCsv: [Bonjour] +After splitCsv: [Holà] +ERROR ~ Error executing process > 'sayHello (2)' + +Caused by: + Missing output file(s) `[Bonjour]-output.txt` expected by process `sayHello (2)` + + +Command executed: + + echo '[Bonjour]' > '[Bonjour]-output.txt' +``` + +This time Nextflow has parsed the contents of the file (yay!) but it's added brackets around the greetings. + +Long story short, `splitCsv()` reads each line into an array, and each comma-separated value in the line becomes an element in the array. +So here it gives us three arrays containing one element each. + +!!! note + + Even if this behavior feels inconvenient right now, it's going to be extremely useful later when we deal with input files with multiple columns of data. + +We could solve this by using `flatten()`, which you already know. +However, there's another operator called `map()` that's more appropriate to use here and is really useful to know; it pops up a lot in Nextflow pipelines. + +### 4.3. Use the `map()` operator to extract the greetings + +The `map()` operator is a very handy little tool that allows us to do all kinds of mappings to the contents of a channel. + +In this case, we're going to use it to extract that one element that we want from each line of our file. +This is what the syntax looks like: + +```groovy title="Syntax" +.map { item -> item[0] } +``` + +This means 'for each item in the channel, take the first of any elements it contains'. + +So let's apply that to our CVS parsing. + +#### 4.3.1. Apply `map()` to the channel + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-channels.nf" linenums="31" +// create a channel for inputs from a CSV file +greeting_ch = Channel.fromPath(params.greeting) + .view { "Before splitCsv: $it" } + .splitCsv() + .view { "After splitCsv: $it" } +``` + +_After:_ + +```groovy title="hello-channels.nf" linenums="31" +// create a channel for inputs from a CSV file +greeting_ch = Channel.fromPath(params.greeting) + .view { "Before splitCsv: $it" } + .splitCsv() + .view { "After splitCsv: $it" } + .map { item -> item[0] } + .view { "After map: $it" } +``` + +Once again we include another `view()` call to confirm that the operator does what we expect. + +#### 4.3.2. Run the workflow one more time + +Let's run it one more time: + +```bash +nextflow run hello-channels.nf +``` + +This time it should run without error. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-channels.nf` [tiny_heisenberg] DSL2 - revision: 845b471427 + +executor > local (3) +[1a/1d19ab] sayHello (2) | 3 of 3 ✔ +Before splitCsv: /workspace/gitpod/hello-nextflow/greetings.csv +After splitCsv: [Hello] +After splitCsv: [Bonjour] +After splitCsv: [Holà] +After map: Hello +After map: Bonjour +After map: Holà +``` + +Looking at the output of the `view()` statements, we see the following: + +- A single `Before splitCsv:` statement: at that point the channel contains one item, the original file path. +- Three separate `After splitCsv:` statements: one for each greeting, but each is contained within an array that corresponds to that line in the file. +- Three separate `After map:` statements: one for each greeting, which are now individual items in the channel. + +You can also look at the output files to verify that each greeting was correctly extracted and processed through the workflow. + +We've achieved the same result as previously, but now we have a lot more flexibility to add more elements to the channel of greetings we want to process by modifying an input file, without modifying any code. + +!!! note + + Here we had all greetings on one line in the CSV file. + You can try adding more columns to the CSV file and see what happens; for example, try the following: + + ```csv title="greetings.csv" + Hello,English + Bonjour,French + Holà,Spanish + ``` + + You can also try replacing `.map { item -> item[0] }` with `.flatten()` and see what happens depending on how many lines and columns you have in the input file. + + You'll learn learn more advanced approaches for handling complex inputs in a later training. + +### Takeaway + +You know how to use the operators `splitCsv()` and `map()` to read in a file of input values and handle them appropriately. + +More generally, you have a basic understanding of how Nextflow uses **channels** to manage inputs to processes and **operators** to transform their contents. + +### What's next? + +Take a big break, you worked hard in this one! +When you're ready, move on to Part 3 to learn how to add more steps and connect them together into a proper workflow. diff --git a/docs/hello_nextflow/02_hello_world.md b/docs/hello_nextflow/02_hello_world.md deleted file mode 100644 index 8d6588d03..000000000 --- a/docs/hello_nextflow/02_hello_world.md +++ /dev/null @@ -1,1186 +0,0 @@ -# Part 1: Hello World - -A "Hello World!" is a minimalist example that is meant to demonstrate the basic syntax and structure of a programming language or software framework. The example typically consists of printing the phrase "Hello, World!" to the output device, such as the console or terminal, or writing it to a file. - -In this first part of the Hello Nextflow training course, we ease into the topic with a very simple domain-agnostic Hello World example, which we'll progressively build up to demonstrate the usage of foundational Nextflow logic and components. - ---- - -## 0. Warmup: Run Hello World directly - -Let's demonstrate this with a simple command that we run directly in the terminal, to show what it does before we wrap it in Nextflow. - -### 0.1. Make the terminal say hello - -```bash -echo 'Hello World!' -``` - -### 0.2. Now make it write the text output to a file - -```bash -echo 'Hello World!' > output.txt -``` - -### 0.3. Verify that the output file is there using the `ls` command - -```bash -ls -``` - -### 0.4. Show the file contents - -```bash -cat output.txt -``` - -!!! tip - - In the Gitpod environment, you can also find the output file in the file explorer, and view its contents by clicking on it. Alternatively, you can use the `code` command to open the file for viewing. - - ```bash - code output.txt - ``` - -### Takeaway - -You now know how to run a simple command in the terminal that outputs some text, and optionally, how to make it write the output to a file. - -### What's next? - -Discover what that would look like written as a Nextflow workflow. - ---- - -## 1. Try the Hello World workflow starter script - -As mentioned in the orientation, we provide you with a fully functional if minimalist workflow script named `hello-world.nf` that does the same thing as before (write out 'Hello World!') but with Nextflow. - -To get you started, we'll first open up the workflow script so you can get a sense of how it's structured, then we'll run it (before trying to make any modifications) to verify that it does what we expect. - -### 1.1. Decipher the code structure - -Let's open the `hello-world.nf` script in the editor pane. - -!!! note - - The file is in the `hello-nextflow` directory, which should be your current working directory. - You can either click on the file in the file explorer, or type `ls` in the terminal and Cmd+Click (MacOS) or Ctrl+Click (PC) on the file to open it. - -```groovy title="hello-world.nf" linenums="1" -#!/usr/bin/env nextflow - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - output: - stdout - - script: - """ - echo 'Hello World!' - """ -} - -workflow { - - // emit a greeting - sayHello() -} -``` - -As you can see, a Nextflow script involves two main types of core components: one or more **processes**, and the **workflow** itself. -Each **process** describes what operation(s) the corresponding step in the pipeline should accomplish, while the **workflow** describes the dataflow logic that connects the various steps. - -Let's take a closer look at the **process** block first, then we'll look at the **workflow** block. - -#### 1.1.1 The `process` definition - -The first block of code describes a **process**. -The process definition starts with the keyword `process`, followed by the process name and finally the process body delimited by curly braces. -The process body must contain a script block which specifies the command to run, which can be anything you would be able to run in a command line terminal. - -Here we have a **process** called `sayHello` that writes its **output** to `stdout`. - -```groovy title="hello-world.nf" linenums="3" -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - output: - stdout - - script: - """ - echo 'Hello World!' - """ -} -``` - -This a very minimal process definition that just contains an output definition and the script itself. -In a real-world pipeline, a process usually contains additional blocks such as directives, inputs, and conditional clauses, which we'll introduce later in this training course. - -!!! note - - The output definition does not _determine_ what output will be created. - It simply _declares_ what is the expected output, so that Nextflow can look for it once execution is complete. - This is necessary for verifying that the command was executed successfully and for passing the output to downstream processes if needed. - -#### 1.1.2 The `workflow` definition - -The second block of code describes the **workflow** itself. -The workflow definition starts with the keyword `workflow`, followed by an optional name, then the workflow body delimited by curly braces. - -Here we have a **workflow** that consists of one call to the `sayHello` process. - -```groovy title="hello-world.nf" linenums="16" -workflow { - - // emit a greeting - sayHello() -} -``` - -This a very minimal **workflow** definition. -In a real-world pipeline, the workflow typically contains multiple calls to **processes** connected by **channels**. -You'll learn how to add more processes and connect them by channels in a little bit. - -### 1.2. Run the workflow - -Looking at code is not nearly as fun as running it, so let's try this out in practice. - -```bash -nextflow run hello-world.nf -``` - -You console output should look something like this: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [reverent_carson] DSL2 - revision: 463b611a35 - -executor > local (1) -[1c/7d08e6] sayHello [100%] 1 of 1 ✔ -``` - -Congratulations, you just ran your first Nextflow workflow! - -The most important output here is the last line (line 6), which reports that the `sayHello` process was successfully executed once. - -Okay, that's great, but where do we find the output? -The `sayHello` process definition said that the output would be sent to standard out, but nothing got printed in the console, did it? - -### 1.3. Find the output and logs in the `work` directory - -When you run Nextflow for the first time in a given directory, it creates a directory called `work` where it will write all files (and symlinks) generated in the course of execution. -Have a look inside; you'll find a subdirectory named with a hash (in order to make it unique; we'll discuss why in a bit), nested two levels deep and containing a handful of log files. - -!!! tip - - If you browse the contents of the task subdirectory in the Gitpod's VSCode file explorer, you'll see all these files right away. - However, these files are set to be invisible in the terminal, so if you want to use `ls` or `tree` to view them, you'll need to set the relevant option for displaying invisible files. - - ```bash - tree -a work - ``` - - You should see something like this, though the exact subdirectory names will be different on your system. - - ```console title="Directory contents" - work - └── 1c - └── 7d08e685a7aa7060b9c21667924824 - ├── .command.begin - ├── .command.err - ├── .command.log - ├── .command.out - ├── .command.run - ├── .command.sh - └── .exitcode - ``` - -You may have noticed that the subdirectory names appeared (in truncated form) in the output from the workflow run, in the line that says: - -```console title="Output" -[1c/7d08e6] sayHello [100%] 1 of 1 ✔ -``` - -This tells you what is the subdirectory path for that specific process call (sometimes called task). - -!!! note - - Nextflow creates a separate unique subdirectory for each process call. - It stages the relevant input files, script, and other helper files there, and writes any output files and logs there as well. - -If we look inside the subdirectory, we find the following log files: - -- **`.command.begin`**: Metadata related to the beginning of the execution of the process task -- **`.command.err`**: Error messages (stderr) emitted by the process task -- **`.command.log`**: Complete log output emitted by the process task -- **`.command.out`**: Regular output (stdout) by the process task -- **`.command.sh`**: The command that was run by the process task call -- **`.exitcode`**: The exit code resulting from the command - -In this case, you can look for your output in the `.command.out` file, since that's where stdout output is captured. -If you open it, you'll find the `Hello World!` greeting, which was the expected result of our minimalist workflow. - -It's also worth having a look at the `.command.sh` file, which tells you what command Nextflow actually executed. In this case it's very straightforward, but later in the course you'll see commands that involve some interpolation of variables. When you're dealing with that, you need to be able to check exactly what was run, especially when troubleshooting an issue. - -### Takeaway - -You know how to decipher a simple Nextflow script, run it and find the output and logs in the work directory. - -### What's next? - -Learn how to make the script output a named file. - ---- - -## 3. Send the output to a file - -Instead of printing "Hello World!" to standard output, we'd prefer to save that output to a specific file, just like we did when running in the terminal earlier. -This is how most tools that you'll run as part of real-world pipelines typically behave; we'll see examples of that later. - -To achieve this result, both the script and the output definition blocks need to be updated. - -### 3.1. Change the process command to output a named file - -This is the same change we made when we ran the command directly in the terminal earlier. - -_Before:_ - -```groovy title="hello-world.nf" linenums="11" -""" -echo 'Hello World!' -""" -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="11" -""" -echo 'Hello World!' > output.txt -""" -``` - -### 3.2. Change the output declaration in the `sayHello` process - -We need to tell Nextflow that it should now look for a specific file to be produced by the process execution. - -_Before:_ - -```groovy title="hello-world.nf" linenums="8" -output: - stdout -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="8" -output: - path 'output.txt' -``` - -!!! note - - Inputs and outputs in the process blocks typically require a qualifier and a variable name: - - ``` - - ``` - - The qualifier defines the type of data to be received. - This information is used by Nextflow to apply the semantic rules associated with each qualifier, and handle it properly. - Common qualifiers include `val` and `path`. - In the example above, `stdout` is an exception since it is not associated with a name. - -### 3.3. Run the workflow again - -```bash -nextflow run hello-world.nf -``` - -The log output should be very similar to the first time your ran the workflow: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [cranky_sinoussi] DSL2 - revision: 30b437bb96 - -executor > local (1) -[7a/6bd54c] sayHello [100%] 1 of 1 ✔ -``` - -Like you did before, find the `work` directory in the file explorer. -There, find the `output.txt` output file and click on it to open it, and verify that it contains the greeting as expected. - -!!! warning - - This example is brittle because we hardcoded the output filename in two separate places (the script and the output blocks). - If we change one but not the other, the script will break. - Later, you'll learn how to use variables to avoid this problem. - -### 3.4. Add a `publishDir` directive to the process - -You'll have noticed that the output is buried in a working directory several layers deep. -Nextflow is in control of this directory and we are not supposed to interact with it. -To make the output file more accessible, we can utilize the `publishDir` directive. -By specifying this directive, we are telling Nextflow to automatically copy the output file to a designated output directory. -This allows us to leave the working directory alone, while still having easy access to the desired output file. - -_Before:_ - -```groovy title="hello-world.nf" linenums="6" -process sayHello { - - output: - path 'output.txt' -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="6" -process sayHello { - - publishDir 'results', mode: 'copy' - - output: - path 'output.txt' -``` - -!!! note - - There is a newer syntax option that makes it possible to declare and publish workflow-level outputs, documented [here](https://www.nextflow.io/docs/latest/workflow.html#publishing-outputs), which makes using `publishDir` at the process level redundant once your pipeline is fully operational. - However, `publishDir` is still very useful during pipeline development; that is why we include it in this training series. - This will also ensure that you can read and understand the large number of pipelines that have already been written with `publishDir`. - - You'll learn how to use the workflow-level outputs syntax later in this training series. - -### 3.5. Run the workflow again - -```bash -nextflow run hello-world.nf -``` - -The log output should start looking very familiar: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [mighty_lovelace] DSL2 - revision: 6654bc1327 - -executor > local (1) -[10/15498d] sayHello [100%] 1 of 1 ✔ -``` - -This time, Nextflow will have created a new directory called `results/`. -In this directory is our `output.txt` file. -If you check the contents it should match the output in our work/task directory. -This is how we move results files outside of the working directories. - -### Takeaway - -You know how to send outputs to a specific named file and use the `publishDir` directive to move files outside of the Nextflow working directory. - -### What's next? - -Learn how to make Nextflow resume running a pipeline using cached results from a prior run to skip any steps it had already completed successfully. - ---- - -## 4. Use the Nextflow resume feature - -Nextflow has an option called `-resume` that allows you to re-run a pipeline you've already launched previously. -When launched with `-resume` any processes that have already been run with the exact same code, settings and inputs will be skipped. -Using this mode means Nextflow will only run processes that are either new, have been modified or are being provided new settings or inputs. - -There are two key advantages to doing this: - -- If you're in the middle of developing your pipeline, you can iterate more rapidly since you only effectively have to run the process(es) you're actively working on in order to test your changes. -- If you're running a pipeline in production and something goes wrong, in many cases you can fix the issue and relaunch the pipeline, and it will resume running from the point of failure, which can save you a lot of time and compute. - -### 4.1. Run the workflow again with `-resume` - -```bash -nextflow run hello-world.nf -resume -``` - -The console output should look similar. - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [thirsty_gautier] DSL2 - revision: 6654bc1327 - -[10/15498d] sayHello [100%] 1 of 1, cached: 1 ✔ -``` - -Notice the additional `cached:` bit in the process status line, which means that Nextflow has recognized that it has already done this work and simply re-used the result from the last run. - -!!! note - - When your re-run a pipeline with `resume`, Nextflow does not overwrite any files written to a publishDir directory by any process call that was previously run successfully. - -### Takeaway - -You know how to to relaunch a pipeline without repeating steps that were already run in an identical way. - -### What's next? - -Learn how to add in variable inputs. - ---- - -## 5. Add in variable inputs using a channel - -So far, we've been emitting a greeting hardcoded into the process command. -Now we're going to add some flexibility by using an input variable, so that we can easily change the greeting. - -This requires us to make a series of inter-related changes: - -1. Tell the process about expected variable inputs using the `input:` block -2. Edit the process to use the input -3. Create a **channel** to pass input to the process (more on that in a minute) -4. Add the channel as input to the process call - -### 5.1. Add an input definition to the process block - -First we need to adapt the process definition to accept an input. - -_Before:_ - -```groovy title="hello-world.nf" linenums="6" -process sayHello { - - publishDir 'results', mode: 'copy' - - output: - path "output.txt" -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="6" -process sayHello { - - publishDir 'results', mode: 'copy' - - input: - val greeting - - output: - path "output.txt" -``` - -### 5.2. Edit the process command to use the input variable - -Now we swap the original hardcoded value for the input variable. - -_Before:_ - -```groovy title="hello-world.nf" linenums="16" -""" -echo 'Hello World!' > output.txt -""" -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="16" -""" -echo '$greeting' > output.txt -""" -``` - -### 5.3. Create an input channel - -Now that our process expects an input, we need to set up that input in the workflow body. -This is where channels come in: Nextflow uses channels to feed inputs to processes and ferry data between processes that are connected together. - -There are multiple ways to do this, but for now, we're just going to use the simplest possible channel, containing a single value. - -We're going to create the channel using the `of()` channel factory, which sets up a simple value channel, and give it a hardcoded string to use as greeting by declaring `greeting_ch = Channel.of('Hello world!')`. - -_Before:_ - -```groovy title="hello-world.nf" linenums="21" -workflow { - - // emit a greeting - sayHello() -} -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="21" -workflow { - - // create a channel for inputs - greeting_ch = Channel.of('Hello world!') - - // emit a greeting - sayHello() -} -``` - -### 5.4. Add the channel as input to the process call - -Now we need to actually plug our newly created channel into the `sayHello()` process call. - -_Before:_ - -```groovy title="hello-world.nf" linenums="26" -// emit a greeting -sayHello() -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="26" -// emit a greeting -sayHello(greeting_ch) -``` - -### 5.5. Run the workflow command again - -Let's run it! - -```bash -nextflow run hello-world.nf -``` - -If you made all four edits correctly, you should get another successful execution: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [prickly_avogadro] DSL2 - revision: b58b6ab94b - -executor > local (1) -[1f/50efd5] sayHello (1) [100%] 1 of 1 ✔ -``` - -Feel free to check the results directory to satisfy yourself that the outcome is still the same as previously; so far we're just progressively tweaking the internal plumbing to increase the flexibility of our workflow while achieving the same end result. - -### Takeaway - -You know how to use a simple channel to provide an input to a process. - -### What's next? - -Learn how to pass inputs from the command line. - ---- - -## 6. Use CLI parameters for inputs - -We want to be able to specify the input from the command line, since that is the piece that will almost always be different in subsequent runs of the workflow. -Good news: Nextflow has a built-in workflow parameter system called `params`, which makes it easy to declare and use CLI parameters. - -### 6.1. Edit the input channel declaration to use a parameter - -Here we swap out the hardcoded string for `params.greeting` in the channel creation line. - -_Before:_ - -```groovy title="hello-world.nf" linenums="23" -// create a channel for inputs -greeting_ch = Channel.of('Hello world!') -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="23" -// create a channel for inputs -greeting_ch = Channel.of(params.greeting) -``` - -This automatically creates a parameter called `greeting` that you can use to provide a value in the command line. - -### 6.2. Run the workflow again with the `--greeting` parameter - -To provide a value for this parameter, simply add `--greeting ` to your command line. - -```bash -nextflow run hello-world.nf --greeting 'Bonjour le monde!' -``` - -Running this should feel extremely familiar by now. - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [cheesy_engelbart] DSL2 - revision: b58b6ab94b - -executor > local (1) -[1c/9b6dc9] sayHello (1) [100%] 1 of 1 ✔ -``` - -Be sure to open up the output file to check that you now have the new version of the greeting. Voilà! - -!!! tip - - It's helpful to distinguish Nextflow-level parameters from pipeline-level parameters. - For parameters that apply to a pipeline, we use a double hyphen (`--`), whereas we use a single hyphen (`-`) for parameters that modify a specific Nextflow setting, _e.g._ the `-resume` feature we used earlier. - -### 6.3. Set a default value for a command line parameter - -In many cases, it makes sense to supply a default value for a given parameter so that you don't have to specify it for every run. - -Let's initialize the `greeting` parameter with a default value by adding the parameter declaration at the top of the script (with a comment block as a free bonus). - -```groovy title="hello-world.nf" linenums="3" -/* - * Pipeline parameters - */ -params.greeting = "Holà mundo!" -``` - -### 6.4. Run the workflow again without specifying the parameter - -Now that you have a default value set, you can run the workflow again without having to specify a value in the command line. - -```bash -nextflow run hello-world.nf -``` - -The output should look the same. - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [wise_waddington] DSL2 - revision: 988fc779cf - -executor > local (1) -[c0/8b8332] sayHello (1) [100%] 1 of 1 ✔ -``` - -Check the output in the results directory, and... Tadaa! It works! Nextflow used the default value to name the output. But wait, what happens now if we provide the parameter in the command line? - -### 6.5. Run the workflow again with the `--greeting` parameter on the command line using a different greeting - -```bash -nextflow run hello-world.nf --greeting 'Konnichiwa!' -``` - -Nextflow's not complaining, that's a good sign: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [prickly_miescher] DSL2 - revision: 988fc779cf - -executor > local (1) -[56/f88a56] sayHello (1) [100%] 1 of 1 ✔ -``` - -Check the results directory and look at the contents of `output.txt`. Tadaa again! - -The value of the parameter we passed on the command line overrode the value we gave the variable in the script. In fact, parameters can be set in several different ways; if the same parameter is set in multiple places, its value is determined based on the order of precedence that is described [here](https://www.nextflow.io/docs/latest/config.html). - -!!! tip - - You can put the parameter declaration inside the workflow block if you prefer. Whatever you choose, try to group similar things in the same place so you don't end up with declarations all over the place. - -### Takeaway - -You know how to set up an input variable for a process and supply a value in the command line. - -### What's next? - -Learn how to add in a second process and chain them together. - ---- - -## 7. Add a second step to the workflow - -Most real-world workflows involve more than one step. Here we introduce a second process that converts the text to uppercase (all-caps), using the classic UNIX one-liner: - -```bash -tr '[a-z]' '[A-Z]' -``` - -We're going to run the command by itself in the terminal first to verify that it works as expected without any of the workflow code getting in the way of clarity, just like we did at the start with `echo 'Hello World'`. Then we'll write a process that does the same thing, and finally we'll connect the two processes so the output of the first serves as input to the second. - -### 7.1. Run the command in the terminal by itself - -```bash -echo 'Hello World' | tr '[a-z]' '[A-Z]' -``` - -The output is simply the uppercase version of the text string: - -```console title="Output" -HELLO WORLD -``` - -!!! note - - This is a very naive text replacement one-liner that does not account for accented letters, so for example 'Holà' will become 'HOLà'. This is expected. - -### 7.2. Make the command take a file as input and write the output to a file - -As previously, we want to output results to a dedicated file, which we name by prepending the original filename with `UPPER-`. - -```bash -cat output.txt | tr '[a-z]' '[A-Z]' > UPPER-output.txt -``` - -Now the `HELLO WORLD` output is in the new output file, `UPPER-output.txt`. - -### 7.3. Wrap the command in a new Nextflow process definition - -We can model our new process on the first one, since we want to use all the same components. - -```groovy title="hello-world.nf" linenums="26" -/* - * Use a text replace utility to convert the greeting to uppercase - */ -process convertToUpper { - - publishDir 'results', mode: 'copy' - - input: - path input_file - - output: - path "UPPER-${input_file}" - - script: - """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file} - """ -} -``` - -As a little bonus, here we composed the second output filename based on the first one. - -!!! tip - - Very important to remember: you have to use double quotes around the output filename expression (NOT single quotes) or it will fail. - -### 7.4. Add a call to the new process in the workflow body - -Don't forget we need to tell Nextflow to actually call the process we just created! To do that, we add it to the `workflow` body. - -```groovy title="hello-world.nf" linenums="44" -workflow { - - // create a channel for inputs - greeting_ch = Channel.of(params.greeting) - - // emit a greeting - sayHello(greeting_ch) - - // convert the greeting to uppercase - convertToUpper() -} -``` - -Looking good! But we still need to wire up the `convertToUpper` process call to run on the output of `sayHello`. - -### 7.5. Pass the output of the first process to the second process - -The output of the `sayHello` process is automatically packaged as a channel called `sayHello.out`, so all we need to do is pass that as the input to the `convertToUpper` process. - -```groovy title="hello-world.nf" linenums="52" -// convert the greeting to uppercase -convertToUpper(sayHello.out) -``` - -For a simple case like this, that's all we need to do to connect two processes! - -### 7.6. Run the same workflow command as before - -Let's make sure this works: - -```bash -nextflow run hello-world.nf --greeting 'Hello World!' -``` - -Oh, how exciting! There is now an extra line in the log output, which corresponds to the new process we just added: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [magical_brenner] DSL2 - revision: 0e18f34798 - -executor > local (2) -[57/3836c0] sayHello (1) [100%] 1 of 1 ✔ -[ee/bb3cc8] convertToUpper (1) [100%] 1 of 1 ✔ -``` - -You'll notice that this time the workflow produced two new work subdirectories; one per process call. -Check out the work directory of the call to the second process, where you should find two different output files listed. If you look carefully, you'll notice one of them (the output of the first process) has a little arrow icon on the right; that signifies it's a symbolic link. -It points to the location where that file lives in the work directory of the first process. -By default, Nextflow uses symbolic links to stage input files whenever possible, to avoid making duplicate copies. - -!!! note - - All we did was connect the output of `sayHello` to the input of `convertToUpper` and the two processes could be run in serial. - Nextflow did the hard work of handling input and output files and passing them between the two commands for us. - This is the power of channels in Nextflow, doing the busywork of connecting our pipeline steps together. - - What's more, Nextflow will automatically determine which call needs to be executed first based on how they're connected, so the order in which they're written in the workflow body does not matter. - However, we do recommend you be kind to your collaborators and to your future self, and try to write them in a logical order! - -### Takeaway - -You know how to add a second step that takes the output of the first step as input. - -### What's next? - -Learn how to make the workflow run on a batch of input values. - ---- - -## 8. Modify the workflow to run on a batch of input values - -Workflows typically run on batches of inputs that are meant to be processed in bulk, so we want to upgrade the workflow to accept multiple input values. - -Conveniently, the `of()` channel factory we've been using is quite happy to accept more than one value, so we don't need to modify that at all; we just have to load more values into the channel. - -### 8.1. Load multiple greetings into the input channel - -To keep things simple, we go back to hardcoding the greetings in the channel factory instead of using a parameter for the input, but we'll improve on that shortly. - -_Before:_ - -```groovy title="hello-world.nf" linenums="46" -// create a channel for inputs -greeting_ch = Channel.of(params.greeting) -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="46" -// create a channel for inputs -greeting_ch = Channel.of('Hello','Bonjour','Holà') -``` - -The documentation tells us this should work. Can it really be so simple? - -### 8.2. Run the command and look at the log output - -Let's try it. - -```bash -nextflow run hello-world.nf -``` - -Well, it certainly seems to run just fine. - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [lonely_pare] DSL2 - revision: b9f1d96905 - -executor > local (6) -[3d/1fe62c] sayHello (2) [100%] 3 of 3 ✔ -[86/695813] convertToUpper (3) [100%] 3 of 3 ✔ -``` - -However... This seems to indicate that '3 of 3' calls were made for each process, which is encouraging, but this only give us one subdirectory path for each. What's going on? - -By default, the ANSI logging system writes the logging from multiple calls to the same process on the same line. Fortunately, we can disable that behavior. - -### 8.3. Run the command again with the `-ansi-log false` option - -To expand the logging to display one line per process call, just add `-ansi-log false` to the command. - -```bash -nextflow run hello-world.nf -ansi-log false -``` - -This time we see all six work subdirectories listed in the output: - -```console title="Output" -N E X T F L O W ~ version 24.02.0-edge -Launching `hello-world.nf` [big_woese] DSL2 - revision: 53f20aeb70 -[62/d81e63] Submitted process > sayHello (1) -[19/507af3] Submitted process > sayHello (2) -[8a/3126e6] Submitted process > sayHello (3) -[12/48a5c6] Submitted process > convertToUpper (1) -[73/e6e746] Submitted process > convertToUpper (2) -[c5/4fedda] Submitted process > convertToUpper (3) -``` - -That's much better; at least for this number of processes. -For a complex workflow, or a large number of inputs, having the full list output to the terminal might get a bit overwhelming. - -That being said, we have another problem. If you look in the `results` directory, there are only two files: `output.txt` and `UPPER-output.txt`! - -```console title="Directory contents" -results -├── output.txt -└── UPPER-output.txt -``` - -What's up with that? Shouldn't we be expecting two files per input greeting, so six files in all? - -You may recall that we hardcoded the output file name for the first process. -This was fine as long as there was only a single call made per process, but when we start processing multiple input values and publishing the outputs into the same directory of results, it becomes a problem. -For a given process, every call produces an output with the same file name, so Nextflow just overwrites the previous output file every time a new one is produced. - -### 8.4. Ensure the output file names will be unique - -Since we're going to be publishing all the outputs to the same results directory, we need to ensure they will have unique names. -Specifically, we need to modify the first process to generate a file name dynamically so that the final file names will be unique. - -So how do we make the file names unique? A common way to do that is to use some unique piece of metadata as part of the file name. -Here, for convenience, we'll just use the greeting itself. - -_Before:_ - -```groovy title="hello-world.nf" linenums="11" -process sayHello { - - publishDir 'results', mode: 'copy' - - input: - val greeting - - output: - path "output.txt" - - script: - """ - echo '$greeting' > "output.txt" - """ -} -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="11" -process sayHello { - - publishDir 'results', mode: 'copy' - - input: - val greeting - - output: - path "${greeting}-output.txt" - - script: - """ - echo '$greeting' > '$greeting-output.txt' - """ -} -``` - -This should produce a unique output file name for every call of each process. - -### 8.5. Run the workflow and look at the results directory - -Let's run it and check that it works. - -```bash -nextflow run hello-world.nf -``` - -Reverting back to the summary view, the output looks like this again: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [jovial_mccarthy] DSL2 - revision: 53f20aeb70 - -executor > local (6) -[03/f007f2] sayHello (1) [100%] 3 of 3 ✔ -[e5/dd2890] convertToUpper (3) [100%] 3 of 3 ✔ -``` - -But more importantly, now we have six new files in addition to the two we already had in the `results` directory: - -```console title="Directory contents" -results -├── Bonjour-output.txt -├── Hello-output.txt -├── Holà-output.txt -├── output.txt -├── UPPER-Bonjour-output.txt -├── UPPER-Hello-output.txt -├── UPPER-Holà-output.txt -└── UPPER-output.txt -``` - -Success! Now we can add as many greetings as we like without worrying about output files being overwritten. - -!!! note - - In practice, naming files based on the input data itself is almost always impractical. The better way to generate dynamic filenames is to use a samplesheet contain relevant metadata (such as unique sample IDs) and create a data structure called a 'map', which we pass to processes, and from which we can grab an appropriate identifier to generate the filenames. - We'll show you how to do that later in this training course. - -### Takeaway - -You know how to feed a batch of multiple input elements through a channel. - -### What's next? - -Learn how to make the workflow take a file as its source of input values. - ---- - -## 9. Modify the workflow to take a file as its source of input values - -It's often the case that, when we want to run on a batch of multiple input elements, the input values are contained in a file. -As an example, we have provided you with a CSV file called `greetings.csv` in the `data/` directory, containing several greetings separated by commas. - -```csv title="greetings.csv" -Hello,Bonjour,Holà -``` - -So we just need to modify our workflow to read in the values from a file like that. - -### 9.1. Set up a CLI parameter with a default value pointing to an input file - -First, let's use the `params` system to set up a new parameter called `input_file`, replacing the now useless `greeting` parameter, with a default value pointing to the `greetings.csv` file. - -_Before:_ - -```groovy title="hello-world.nf" linenums="6" -/* - * Pipeline parameters - */ -params.greeting = "Holà mundo!" -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="6" -/* - * Pipeline parameters - */ -params.input_file = "data/greetings.csv" -``` - -### 9.2. Update the channel declaration to handle the input file - -At this point we introduce a new channel factory, `fromPath()`, which has some built-in functionality for handling file paths. -We're going to use that instead of the `of()` channel factory we used previously; the base syntax looks like this: - -```groovy title="channel construction syntax" -Channel.fromPath(params.input_file) -``` - -Now, we are going to deploy a new concept, an 'operator' to transform that CSV file into channel content. You'll learn more about operators later, but for now just understand them as ways of transforming channels in a variety of ways. - -Since our goal is to read in the contents of a `.csv` file, we're going to add the `.splitCsv()` operator to make Nextflow parse the file contents accordingly, as well as the `.flatten()` operator to turn the array element produced by `.splitCsv()` into a channel of individual elements. - -So the channel construction instruction becomes: - -```groovy title="channel construction syntax" -Channel.fromPath(params.input_file) - .splitCsv() - .flatten() -``` - -And here it is in the context of the workflow body: - -_Before:_ - -```groovy title="hello-world.nf" linenums="46" -// create a channel for inputs -greeting_ch = Channel.of('Hello','Bonjour','Holà') -``` - -_After:_ - -```groovy title="hello-world.nf" linenums="46" -// create a channel for inputs from a CSV file -greeting_ch = Channel.fromPath(params.input_file) - .splitCsv() - .flatten() -``` - -If you want to see the impact of `.flatten()`, we can make use of `.view()`, another operator, to demonstrate. Edit that section of code so it looks like: - -```groovy title="flatten usage" -// create a channel for inputs from a CSV file -greeting_ch = Channel.fromPath(params.input_file) - .splitCsv() - .view{ "After splitCsv: $it" } - .flatten() - .view{ "After flatten: $it" } -``` - -When you run this updated workflow, you'll see the difference: - -```console title="view output with and without flatten" -After splitCsv: [Hello, Bonjour, Holà] -After flatten: Hello -After flatten: Bonjour -After flatten: Holà -[d3/1a6e23] Submitted process > sayHello (3) -[8f/d9e431] Submitted process > sayHello (1) -[e7/a088af] Submitted process > sayHello (2) -[1a/776e2e] Submitted process > convertToUpper (1) -[83/fb8eba] Submitted process > convertToUpper (2) -[ee/280f93] Submitted process > convertToUpper (3) -``` - -As you can see, the `flatten()` operator has transformed the channel from containing arrays to containing individual elements. This can be useful when you want to process each item separately in your workflow. - -Remove the `.view()` operations before you continue. - -!!! tip - - While you're developing your pipeline, you can inspect the contents of any channel by adding the `.view()` operator to the name of the channel. - For example, if you add `greeting_ch.view()` anywhere in the workflow body, when you run the script, Nextflow will print the channel contents to standard out. - - You can also use this to inspect the effect of the operators. - For example, the output of `Channel.fromPath(params.input_file).splitCsv().view()` will look like this: - - ```console title="Output" - [Hello, Bonjour, Holà] - ``` - - While the output of `Channel.fromPath(params.input_file).splitCsv().flatten().view()` will look like this: - - ```console title="Output" - Hello - Bonjour - Holà - ``` - -### 9.3. Run the workflow (one last time!) - -```bash -nextflow run hello-world.nf -``` - -Once again we see each process get executed three times: - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `hello-world.nf` [angry_spence] DSL2 - revision: d171cc0193 - -executor > local (6) -[0e/ceb175] sayHello (2) [100%] 3 of 3 ✔ -[01/046714] convertToUpper (3) [100%] 3 of 3 ✔ -``` - -Looking at the outputs, we see each greeting was correctly extracted and processed through the workflow. We've achieved the same result as the previous step, but now we have a lot more flexibility to add more elements to the channel of greetings we want to process. - -### Takeaway - -You know how to provide the input values to the workflow via a file. - -More generally, you've learned how to use the essential components of Nextflow and you have a basic grasp of the logic of how to build a workflow and manage inputs and outputs. - -### What's next? - -Celebrate your success and take a break! - -Don't worry if the channel types and operators feel like a lot to grapple with the first time you encounter them. -You'll get more opportunities to practice using these components in various settings as you work through this training course. - -When you're ready, move on to Part 2 to learn about another important concept: provisioning the software required for each process. diff --git a/docs/hello_nextflow/03_hello_containers.md b/docs/hello_nextflow/03_hello_containers.md deleted file mode 100644 index ec975b17a..000000000 --- a/docs/hello_nextflow/03_hello_containers.md +++ /dev/null @@ -1,471 +0,0 @@ -# Part 2: Hello Containers - -In Part 1, you learned how to use the basic building blocks of Nextflow to assemble a simple pipeline capable of processing some text and parallelizing execution if there were multiple inputs. - -However, you were limited to basic UNIX tools available in your environment. -Real-world tasks often require various tools and packages not included by default. -Typically, you'd need to install these tools, manage their dependencies, and resolve any conflicts. - -That is all very tedious and annoying, so we're going to show you how to use **containers** to solve this problem much more conveniently. - -!!! Note - - We'll be teaching this using the technology [Docker](https://www.docker.com/get-started/), but Nextflow supports [several other container technologies](https://www.nextflow.io/docs/latest/container.html#) as well. - ---- - -## 1. Use a container directly - -A **container** is a lightweight, standalone, executable unit of software created from a container **image** that includes everything needed to run an application including code, system libraries and settings. -To use a container you usually download or "pull" a container image from a container registry, and then run the container image to create a container instance. - -### 1.1. Pull the container image - -Let's pull a container image that contains the `cowsay` command so we can use it to display some text in a fun way. - -```bash -docker pull 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' -``` - -### 1.2 Use the container to execute a single command - -The `docker run` command is used to spin up a container instance from a container image and execute a command in it. -The `--rm` flag tells Docker to remove the container instance after the command has completed. - -```bash -docker run --rm 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' cowsay -t "Hello World" -``` - -```console title="Output" - _____________ -< Hello World > - ------------- - \ ^__^ - \ (oo)\_______ - (__)\ )\/\ - ||----w | - || || -``` - -### 1.2. Spin up the container interactively - -You can also run a container interactively, which will give you a shell prompt inside the container. - -```bash -docker run --rm -it 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' /bin/bash -``` - -Notice that the prompt has changed to `(base) root@b645838b3314:/tmp#`, which indicates that you are now inside the container. -If we run: - -```console title="Output" -(base) root@b645838b3314:/tmp# ls / -bin dev etc home lib media mnt opt proc root run sbin srv sys tmp usr var -``` - -You can see that the filesystem inside the container is different from the filesystem on your host system. - -### 1.3. Run the command - -Now that you are inside the container, you can run the `cowsay` command directly. - -!!! Tip - - Us the '-c' flag to pick a different "cow" from this list: - `beavis`, `cheese`, `cow`, `daemon`, `dragon`, `fox`, `ghostbusters`, `kitty`, `meow`, `miki`, `milk`, `octopus`, `pig`, `stegosaurus`, `stimpy`, `trex`, `turkey`, `turtle`, `tux` - -```bash -cowsay -t "Hello World" -c tux -``` - -Output: - -```console title="Output" - ___________ -| Hello World | - =========== - \ - \ - \ - .--. - |o_o | - |:_/ | - // \ \ - (| | ) - /'\_ _/`\ - \___)=(___/ -``` - -### 1.4. Exit the container - -To exit the container, you can type `exit` at the prompt or use the ++ctrl+d++ keyboard shortcut. - -```bash -exit -``` - -Your prompt should now be back to what it was before you started the container. - -### 1.5. Mounting data into containers - -When you run a container, it is isolated from the host system by default. -This means that the container can't access any files on the host system unless you explicitly tell it to. -One way to do this is to **mount** a **volume** from the host system into the container. - -Prior to working on the next task, confirm that you are in the `hello-nextflow` directory. The last part of the path shown when you type `pwd` should be `hello-nextflow`. - -Then run: - -```bash -docker run --rm -it -v $(pwd)/containers/data:/data 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' /bin/bash -``` - -Let's explore the contents of the container. -Note that we need to navigate to the `/data` directory inside the container to see the contents of the `data` directory on the host system. - -```console title="Output" -(base) root@08dd2d3efbd4:/tmp# ls -conda.yml environment.lock -(base) root@08dd2d3efbd4:/tmp# cd /data -(base) root@08dd2d3efbd4:/data# ls -greetings.csv pioneers.csv -``` - -### 1.6. Use the mounted data - -Now that we have mounted the `data` directory into the container, we can use the `cowsay` command to display the contents of the `greetings.csv` file. -To do this we'll use the syntax `-t "$(cat data/greetings.csv)"` to output the contents of the file into the `cowsay` command. - -```bash -cowsay -t "$(cat /data/greetings.csv)" -c pig -``` - -Output: - -```console title="Output" - __________________ -| Hello,Bonjour,Holà | - ================== - \ - \ - \ - \ - ,. - (_|,. - ,' /, )_______ _ - __j o``-' `.'-)' - (") \' - `-j | - `-._( / - |_\ |--^. / - /_]'|_| /_)_/ - /_]' /_]' -``` - -Now exit the container once again: - -```bash -exit -``` - -### Takeaway - -You know how to pull a container and run it interactively, make your data accessible to it, which lets you try commands without having to install any software on your system. - -### What's next? - -Learn how to get a container image for any pip/conda-installable tool. - ---- - -## 2. Use containers in Nextflow - -Nextflow has built-in support for running processes inside containers to let you run tools you don't have installed in your compute environment. -This means that you can use any container image you like to run your processes, and Nextflow will take care of pulling the image, mounting the data, and running the process inside it. - -### 2.1. Add a container directive to your process - -Edit the `hello-containers.nf` script to add a `container` directive to the `cowsay` process. - -_Before:_ - -```groovy title="hello-containers.nf" -process cowSay { - - publishDir 'containers/results', mode: 'copy' -``` - -_After:_ - -```groovy title="hello-containers.nf" -process cowSay { - - publishDir 'containers/results', mode: 'copy' - container 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' -``` - -### 2.2. Run Nextflow pipelines using containers - -Run the script to see the container in action. - -```bash -nextflow run hello-containers.nf -``` - -!!! NOTE - - The `nextflow.config` in our current working directory contains `docker.enabled = true`, which tells Nextflow to use Docker to run processes. - Without that configuration we would have to specify the `-with-docker` flag when running the script. - -### 2.3. Check the results - -You should see a new directory called `containers/results` that contains the output of the `cowsay` process. - -```console title="containers/results/cowsay-output-Bonjour.txt" - _______ -| Bonjour | - ======= - \ - \ - ^__^ - (oo)\_______ - (__)\ )\/\ - ||----w | - || || -``` - -### 2.4. Explore how Nextflow launched the containerized task - -Let's take a look at the task directory for one of the cowsay tasks to see how Nextflow works with containers under the hood. - -Check the output from your `nextflow run` command to find the task ID for the `cowsay` process. -Then check out the task directory for that task. - -```bash -tree -a work/8c/738ac55b80e7b6170aa84a68412454 -work/8c/738ac55b80e7b6170aa84a68412454 -├── .command.begin -├── .command.err -├── .command.log -├── .command.out -├── .command.run -├── .command.sh -├── .exitcode -├── cowsay-output-Bonjour.txt -└── output-Bonjour.txt -> /workspace/gitpod/nf-training/hello-nextflow/work/0e/e96c123cb7ae9ff7b7bed1c5444009/output-Bonjour.txt - -1 directory, 9 files -``` - -Open the `.command.run` file which holds all the busywork that Nextflow does under the hood. - -```bash -code work/8c/738ac55b80e7b6170aa84a68412454/.command.run -``` - -Search for `nxf_launch` and you should see something like this: - -```bash -nxf_launch() { - docker run -i --cpu-shares 1024 -e "NXF_TASK_WORKDIR" -v /workspace/gitpod/nf-training/hello-nextflow/work:/workspace/gitpod/nf-training/hello-nextflow/work -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65 /bin/bash -ue /workspace/gitpod/nf-training/hello-nextflow/work/8c/738ac55b80e7b6170aa84a68412454/.command.sh -} -``` - -As you can see, Nextflow is using the `docker run` command to launch the task. -It also mounts the task's working directory into the container, sets the working directory inside the container to the task's working directory, and runs our templated bash script in the `.command.sh` file. -All the hard work we learned about in the previous sections is done for us by Nextflow! - -### Takeaway - -You know how to use containers in Nextflow to run processes. - -### What's next? - -You have everything you need to continue to the [next chapter](./04_hello_genomics.md) of this training series. -Optionally, continue on to learn how to get container images for tools you want to use in your Nextflow pipelines. - ---- - -## 3. Optional Topic: How to find or make container images - -Some software developers provide container images for their software that are available on container registries like Docker Hub, but many do not. -In this optional section, we'll show you to two ways to get a container image for tools you want to use in your Nextflow pipelines: using Seqera Containers and building the container image yourself. - -You'll be getting/building a container image for the `quote` pip package, which will be used in the exercise at the end of this section. - -### 3.1. Get a container image from Seqera Containers - -Seqera Containers is a free service that builds container images for pip and conda (including bioconda) installable tools. -Navigate to [Seqera Containers](https://www.seqera.io/containers/) and search for the `quote` pip package. - -![Seqera Containers](img/seqera-containers-1.png) - -Click on "+Add" and then "Get Container" to request a container image for the `quote` pip package. - -![Seqera Containers](img/seqera-containers-2.png) - -If this is the first time a community container has been built for this version of the package, it may take a few minutes to complete. -Click to copy the URI (e.g. `community.wave.seqera.io/library/pip_quote:ae07804021465ee9`) of the container image that was created for you. - -You can now use the container image to run the `quote` command and get a random saying from Grace Hopper. - -```bash -docker run --rm community.wave.seqera.io/library/pip_quote:ae07804021465ee9 quote "Grace Hopper" -``` - -Output: - -```console title="Output" -Humans are allergic to change. They love to say, 'We've always done it -this way.' I try to fight that. That's why I have a clock on my wall -that runs counter-clockwise. -``` - -### 3.2. Build the container image yourself - -Let's use some build details from the Seqera Containers website to build the container image for the `quote` pip package ourselves. -Return to the Seqera Containers website and click on the "Build Details" button. - -The first item we'll look at is the `Dockerfile`, a type of script file that contains all the commands needed to build the container image. -We've added some explanatory comments to the Dockerfile below to help you understand what each part does. - -```Dockerfile title="Dockerfile" -# Start from the micromamba base docker image -FROM mambaorg/micromamba:1.5.10-noble -# Copy the conda.yml file into the container -COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml -# Install various utilities for Nextflow to use and the packages in the conda.yml file -RUN micromamba install -y -n base -f /tmp/conda.yml \ - && micromamba install -y -n base conda-forge::procps-ng \ - && micromamba env export --name base --explicit > environment.lock \ - && echo ">> CONDA_LOCK_START" \ - && cat environment.lock \ - && echo "<< CONDA_LOCK_END" \ - && micromamba clean -a -y -# Run the container as the root user -USER root -# Set the PATH environment variable to include the micromamba installation directory -ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH" -``` - -The second item we'll look at is the `conda.yml` file, which contains the list of packages that need to be installed in the container image. - -```conda.yml title="conda.yml" -channels: -- conda-forge -- bioconda -dependencies: -- pip -- pip: - - quote==3.0.0 # -``` - -Copy the contents of these files into the stubs located in the `containers/build` directory, then run the following command to build the container image yourself. - -!!! Note - - We use the `-t quote:latest` flag to tag the container image with the name `quote` and the tag `latest`. - We will be able to use this tag to refer to the container image when running it on this system. - -```bash -docker build -t quote:latest containers/build -``` - -After it has finished building, you can run the container image you just built. - -```bash -docker run --rm quote:latest quote "Margaret Oakley Dayhoff" -``` - -### Takeaway - -You've learned two different ways to get a container image for a tool you want to use in your Nextflow pipelines: using Seqera Containers and building the container image yourself. - -### What's next? - -You have everything you need to continue to the [next chapter](./04_hello_genomics.md) of this training series. -You can also continue on with an optional exercise to fetch quotes on computer/biology pioneers using the `quote` container and output them using the `cowsay` container. - ---- - -## 4. Bonus Exercise: Make the cow quote famous scientists - -This section contains some stretch exercises, to practice what you've learned so far. -Doing these exercises is _not required_ to understand later parts of the training, but provide a fun way to reinforce your learnings by figuring out how to make the cow quote famous scientists. - -```console title="cowsay-output-Grace-Hopper.txt" - _________________________________________________ - / \ -| Humans are allergic to change. They love to | -| say, 'We've always done it this way.' I try to fi | -| ght that. That's why I have a clock on my wall th | -| at runs counter-clockwise. | -| -Grace Hopper | - \ / - ================================================= - \ - \ - ^__^ - (oo)\_______ - (__)\ )\/\ - ||----w | - || || -``` - -### 4.1. Modify the `hello-containers.nf` script to use a getQuote process - -We have a list of computer and biology pioneers in the `containers/data/pioneers.csv` file. -At a high level, to complete this exercise you will need to: - -- Modify the default `params.input_file` to point to the `pioneers.csv` file. -- Create a `getQuote` process that uses the `quote` container to fetch a quote for each input. -- Connect the output of the `getQuote` process to the `cowsay` process to display the quote. - -For the `quote` container image, you can either use the one you built yourself in the previous stretch exercise or use the one you got from Seqera Containers . - -!!! Hint - - A good choice for the `script` block of your getQuote process might be: - ```groovy - script: - def safe_author = author.tokenize(' ').join('-') - """ - quote "$author" > quote-${safe_author}.txt - echo "-${author}" >> quote-${safe_author}.txt - """ - ``` - -You can find a solution to this exercise in `containers/solutions/hello-containers-4.1.nf`. - -### 4.2. Modify your Nextflow pipeline to allow it to execute in `quote` and `sayHello` modes. - -Add some branching logic using to your pipeline to allow it to accept inputs intended for both `quote` and `sayHello`. -Here's an example of how to use an `if` statement in a Nextflow workflow: - -```groovy title="hello-containers.nf" -workflow { - if (params.quote) { - ... - } - else { - ... - } - cowSay(text_ch) -} -``` - -!!! Hint - - You can use `new_ch = processName.out` to assign a name to the output channel of a process. - -You can find a solution to this exercise in `containers/solutions/hello-containers-4.2.nf`. - -### Takeaway - -You know how to use containers in Nextflow to run processes, and how to build some branching logic into your pipelines! - -### What's next? - -Celebrate, take a stretch break and drink some water! - -When you are ready, move on to Part 3 of this training series to learn how to apply what you've learned so far to a more realistic data analysis use case. diff --git a/docs/hello_nextflow/03_hello_workflow.md b/docs/hello_nextflow/03_hello_workflow.md new file mode 100644 index 000000000..665d3e8a3 --- /dev/null +++ b/docs/hello_nextflow/03_hello_workflow.md @@ -0,0 +1,861 @@ +# Part 3: Hello Workflow + +Most real-world workflows involve more than one step. +In this training module, you'll learn how to connect processes together in a multi-step workflow. + +This will teach you the Nextflow way of achieving the following: + +1. Making data flow from one process to the next +2. Collecting outputs from multiple process calls into a single process call +3. Passing more than one input to a process +4. Handling multiple outputs coming out of a process + +To demonstrate, we will continue building on the domain-agnostic Hello World example from Parts 1 and 2. +This time, we're going to make the following changes to our workflow to better reflect how people build actual workflows: + +1. Add a second step that converts the greeting to uppercase. +2. Add a third step that collects all the transformed greetings and writes them into a single file. +3. Add a parameter to name the final output file and pass that as a secondary input to the collection step. +4. Make the collection step also output a simple statistic about what was processed. + +--- + +## 0. Warmup: Run `hello-workflow.nf` + +We're going to use the workflow script `hello-workflow.nf` as a starting point. +It is equivalent to the script produced by working through Part 2 of this training course. + +Just to make sure everything is working, run the script once before making any changes: + +```bash +nextflow run hello-workflow.nf +``` + +```console title="Output" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-workflow.nf` [stupefied_sammet] DSL2 - revision: b9e466930b + +executor > local (3) +[2a/324ce6] sayHello (3) | 3 of 3 ✔ +``` + +As previously, you will find the output files in the `results` directory (specified by the `publishDir` directive). + +```console title="Directory contents" +results +├── Bonjour-output.txt +├── Hello-output.txt +└── Holà-output.txt +``` + +!!! note + + There may also be a file named `output.txt` left over if you worked through Part 2 in the same environment. + +If that worked for you, you're ready to learn how to assemble a multi-step workflow. + +--- + +## 1. Add a second step to the workflow + +We're going to add a step to convert the greeting to uppercase. +To that end, we need to do three things: + +- Define the command we'lre going to use to do the uppercase conversion. +- Write a new process that wraps the uppercasing command. +- Add the new process to the workflow and set it up to take the output of the `sayHello()` process as input. + +### 1.1. Define the uppercasing command and test it in the terminal + +To do the conversion of the greetings to uppercase, we're going to a classic UNIX tool called `tr` for 'text replacement', with the following syntax: + +```bash title="Syntax" +tr '[a-z]' '[A-Z]' +``` + +This is a very naive text replacement one-liner that does not account for accented letters, so for example 'Holà' will become 'HOLà', but it will do a good enough job for demonstrating the Nextflow concepts and that's what matters. + +To test it out, we can run the `echo 'Hello World'` command and pipe its output to the `tr` command: + +```bash +echo 'Hello World' | tr '[a-z]' '[A-Z]' > UPPER-output.txt +``` + +The output is a text file called `UPPER-output.txt` that contains the uppercase version of the `Hello World` string: + +```console title="UPPER-output.txt" +HELLO WORLD +``` + +That's basically what we're going to try to do with our workflow. + +### 1.1. Write the uppercasing step as a Nextflow process + +We can model our new process on the first one, since we want to use all the same components. + +Add the following process definition to the workflow script: + +```groovy title="hello-workflow.nf" linenums="22" +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} +``` + +Here, we compose the second output filename based on the input filename, similarly to what we did originally for the output of the first process. + +!!! note + + Nextflow will determine the order of operations based on the chaining of inputs and outputs, so the order of the process definitions in the workflow script does not matter. + However, we do recommend you be kind to your collaborators and to your future self, and try to write them in a logical order for the sake of readability. + +### 1.2. Add a call to the new process in the workflow block + +Now we need to tell Nextflow to actually call the process that we just defined. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="53" + // emit a greeting + sayHello(greeting_ch) +} +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="53" + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper() +} +``` + +This is not yet functional because we have not specified what should be input to the `convertToUpper()` process. + +### 1.3. Pass the output of the first process to the second process + +Now we need to make the output of the `sayHello()` process flow into the `convertToUpper()` process. + +Conveniently, Nextflow automatically packages the output of a process into a channel called `.out`. +So the output of the `sayHello` process is a channel called `sayHello.out`, which we can plug straight into the call to `convertToUpper()`. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="56" + // convert the greeting to uppercase + convertToUpper() +} +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="56" + // convert the greeting to uppercase + convertToUpper(sayHello.out) +} +``` + +For a simple case like this (one output to one input), that's all we need to do to connect two processes! + +### 1.4. Run the workflow again with `-resume` + +Let's run this using the `-resume` flag, since we've already run the first step of the workflow successfully. + +```bash +nextflow run hello-workflow.nf -resume +``` + +You should see the following output: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-workflow.nf` [disturbed_darwin] DSL2 - revision: 4e252c048f + +executor > local (3) +[79/33b2f0] sayHello (2) | 3 of 3, cached: 3 ✔ +[b3/d52708] convertToUpper (3) | 3 of 3 ✔ +``` + +There is now an extra line in the console output (line 7), which corresponds to the new process we just added. + +Let's have a look inside the work directory of one of the calls to the second process. + +```console title="Directory contents" +work/b3/d52708edba8b864024589285cb3445/ +├── Bonjour-output.txt -> /workspace/gitpod/hello-nextflow/work/79/33b2f0af8438486258d200045bd9e8/Bonjour-output.txt +└── UPPER-Bonjour-output.txt +``` + +We find two output files: the output of the first process AND the output of the second. + +The output of the first process is in there because Nextflow staged it there in order to have everything needed for execution within the same subdirectory. +However, it is actually a symbolic link pointing to the the original file in the subdirectory of the first process call. +By default, when running on a single machine as we're doing here, Nextflow uses symbolic links rather than copies to stage input and intermediate files. + +You'll also find the final outputs in the `results` directory since we used the `publishDir` directive in the second process too. + +```console title="Directory contents" +results +├── Bonjour-output.txt +├── Hello-output.txt +├── Holà-output.txt +├── UPPER-Bonjour-output.txt +├── UPPER-Hello-output.txt +└── UPPER-Holà-output.txt +``` + +Think about how all we did was connect the output of `sayHello` to the input of `convertToUpper` and the two processes could be run in series. +Nextflow did the hard work of handling individual input and output files and passing them between the two commands for us. + +This is one of the reasons Nextflow channels are so powerful: they take care of the busywork involved in connecting workflow steps together. + +### Takeaway + +You know how to add a second step that takes the output of the first step as input. + +### What's next? + +Learn how to collect outputs from batched process calls and feed them into a single process. + +--- + +## 2. Add a third step to collect all the greetings + +When we use a process to apply a transformation to each of the elements in a channel, like we're doing here to the multiple greetings, we sometimes want to collect elements from the output channel of that process, and feed them into another process that performs some kind of analysis or summation. + +In the next step we're simply going to write all the elements of a channel to a single file, using the UNIX `cat` command. + +### 2.1. Define the collection command and test it in the terminal + +The collection step we want to add to our workflow will use the `cat` command to concatenate multiple uppercased greetings into a single file. + +Let's run the command by itself in the terminal to verify that it works as expected, just like we've done previously. + +Run the following in your terminal: + +```bash +echo 'Hello' | tr '[a-z]' '[A-Z]' > UPPER-Hello-output.txt +echo 'Bonjour' | tr '[a-z]' '[A-Z]' > UPPER-Bonjour-output.txt +echo 'Holà' | tr '[a-z]' '[A-Z]' > UPPER-Holà-output.txt +cat UPPER-Hello-output.txt UPPER-Bonjour-output.txt UPPER-Holà-output.txt > COLLECTED-output.txt +``` + +The output is a text file called `COLLECTED-output.txt` that contains the uppercase versions of the original greetings. + +```console title="COLLECTED-output.txt" +HELLO +BONJOUR +HOLà +``` + +That is the result we want to achieve with our workflow. + +### 2.1. Create a new process to do the collection step + +Let's create a new process and call it `collectGreetings()`. +We can start writing it based on the previous one. + +#### 2.1.1. Write the 'obvious' parts of the process + +Add the following process definition to the workflow script: + +```groovy title="hello-workflow.nf" linenums="41" +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + ??? + + output: + path "COLLECTED-output.txt" + + script: + """ + ??? > 'COLLECTED-output.txt' + """ +} +``` + +This is what we can write with confidence based on what you've learned so far. +But this is not functional! +It leaves out the input definition(s) and the first half of the script command because we need to figure out how to write that. + +### 2.1.2. Define inputs to `collectGreetings()` + +We need to collect the greetings from all the calls to the `convertToUpper()` process. +What do we know we can get from the previous step in the workflow? + +The channel output by `convertToUpper()` will contain the paths to the individual files containing the uppercased greetings. +That amounts to one input slot; let's call it `input_files` for simplicity. + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="48" + input: + ??? +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="48" + input: + path input_files +``` + +Notice we use the `path` prefix even though we expect this to contain multiple files. +Nextflow doesn't mind, so it doesn't matter. + +#### 2.1.3. Compose the concatenation command + +This is where things could get a little tricky, because we need to be able to handle an arbitrary number of input files. +Specifically, we can't write the command up front, so we need to tell Nextflow how to compose it at runtime based on what inputs flow into the process. + +In other words, if we have an input channel containing the item `[file1.txt, file2.txt, file3.txt]`, we need Nextflow to turn that into `cat file1.txt file2.txt file3.txt`. + +Fortunately, Nextflow is quite happy to do that for us if we simply write `cat ${input_files}` in the script command. + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="54" + script: + """ + ??? > 'COLLECTED-output.txt' + """ +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="54" + script: + """ + cat ${input_files} > 'COLLECTED-output.txt' + """ +``` + +In theory this should handle any arbitrary number of input files. + +!!! tip + + Some command-line tools require providing an argument (like `-input`) for each input file. + In that case, we would have to do a little bit of extra work to compose the command. + You can see an example of this in the 'Nextflow for Genomics' training course. + + + +### 2.2. Add the collection step to the workflow + +Now we should just need to call the collection process on the output of the uppercasing step. + +#### 2.2.1. Connect the process calls + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="75" + // convert the greeting to uppercase + convertToUpper(sayHello.out) +} +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="75" + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out) +} +``` + +This connects the output of `convertToUpper()` to the input of `collectGreetings()`. + +#### 2.2.2. Run the workflow with `-resume` + +Let's try it. + +```bash +nextflow run hello-workflow.nf -resume +``` + +It runs successfully, including the third step: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-workflow.nf` [mad_gilbert] DSL2 - revision: 6acfd5e28d + +executor > local (3) +[79/33b2f0] sayHello (2) | 3 of 3, cached: 3 ✔ +[99/79394f] convertToUpper (3) | 3 of 3, cached: 3 ✔ +[47/50fe4a] collectGreetings (1) | 3 of 3 ✔ +``` + +However, look at the number of calls for `collectGreetings()` on line 8. +We were only expecting one, but there are three. + +And have a look at the contents of the final output file too: + +```console title="COLLECTED-output.txt" +Holà +``` + +Oh no. The collection step was run individually on each greeting, which is NOT what we wanted. + +We need to do something to tell Nextflow explicitly that we want that third step to run on all the items in the channel output by `convertToUpper()`. + +### 2.3. Use an operator to collect the greetings into a single input + +Yes, once again the answer to our problem is an operator. + +Specifically, we are going to use the aptly-named [`collect()`](https://www.nextflow.io/docs/latest/reference/operator.html#collect) operator. + +#### 2.3.1. Add the `collect()` operator + +This time it's going to look a bit different because we're not adding the operator in the context of a channel factory, but to an output channel. + +We take the `convertToUpper.out` and append the `collect()` operator, which gives us `convertToUpper.out.collect()`. +We can plug that directly into the `collectGreetings()` process call. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="78" + // collect all the greetings into one file + collectGreetings(convertToUpper.out) +} +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="78" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect()) +} +``` + +#### 2.3.2. Add some `view()` statements + +Let's also include a couple of `view()` statements to visualize the before and after states of the channel contents. + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="78" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect()) +} +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="78" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect()) + + // optional view statements + convertToUpper.out.view { "Before collect: $it" } + convertToUpper.out.collect().view { "After collect: $it" } +} +``` + +The `view()` statements can go anywhere you want; we put them after the call for readability. + +#### 2.3.3. Run the workflow again with `-resume` + +Let's try it: + +```bash +nextflow run hello-workflow.nf -resume +``` + +It runs successfully, although the log output may look a little messier than this (we cleaned it up for readability). + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-workflow.nf` [soggy_franklin] DSL2 - revision: bc8e1b2726 + +[d6/cdf466] sayHello (1) | 3 of 3, cached: 3 ✔ +[99/79394f] convertToUpper (2) | 3 of 3, cached: 3 ✔ +[1e/83586c] collectGreetings | 1 of 1 ✔ +Before collect: /workspace/gitpod/hello-nextflow/work/b3/d52708edba8b864024589285cb3445/UPPER-Bonjour-output.txt +Before collect: /workspace/gitpod/hello-nextflow/work/99/79394f549e3040dfc2440f69ede1fc/UPPER-Hello-output.txt +Before collect: /workspace/gitpod/hello-nextflow/work/aa/56bfe7cf00239dc5badc1d04b60ac4/UPPER-Holà-output.txt +After collect: [/workspace/gitpod/hello-nextflow/work/b3/d52708edba8b864024589285cb3445/UPPER-Bonjour-output.txt, /workspace/gitpod/hello-nextflow/work/99/79394f549e3040dfc2440f69ede1fc/UPPER-Hello-output.txt, /workspace/gitpod/hello-nextflow/work/aa/56bfe7cf00239dc5badc1d04b60ac4/UPPER-Holà-output.txt] +``` + +This time the third step was only called once! + +Looking at the output of the `view()` statements, we see the following: + +- Three `Before collect:` statements, one for each greeting: at that point the file paths are individual items in the channel. +- A single `After collect:` statement: the three file paths are now packaged into a single item. + +Have a look at the contents of the final output file too: + +```console title="COLLECTED-output.txt" +BONJOUR +HELLO +HOLà +``` + +This time we have all three greetings in the final output file. Success! + +!!! note + + If you run this several times without `-resume`, you will see that the order of the greetings changes from one run to the next. + This shows you that the order in which items flow through the pipeline is not guaranteed to be consistent. + +### Takeaway + +You know how to collect outputs from a batch of process calls and feed them into a joint analysis or summation step. + +### What's next? + +Learn how to pass more than one input to a process. + +--- + +## 3. Pass more than one input to a process in order to name the final output file uniquely + +We want to be able to name the final output file something specific in order to process subsequent batches of greetings without overwriting the final results. + +To that end, we're going to make the following refinements to the workflow: + +- Modify the collector process to accept a user-defined name for the output file +- Add a command-line parameter to the workflow and pass it to the collector process + +### 3.1. Modify the collector process to accept a user-defined name for the output file + +We're going to need to declare the additional input and integrate it into the output file name. + +#### 3.1.1. Declare the additional input in the process definition + +Good news: we can declare as many input variables as we want. +Let's call this one `batch_name`. + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="48" + input: + path input_files +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="48" + input: + path input_files + val batch_name +``` + +You can set up your processes to expect as many inputs as you want. +Later on, you will learn how to manage required vs. optional inputs. + +#### 3.1.2. Use the `batch_name` variable in the output file name + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="52" + output: + path "COLLECTED-output.txt" + + script: + """ + cat ${input_files} > 'COLLECTED-output.txt' + """ +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="52" + output: + path "COLLECTED-${batch_name}-output.txt" + + script: + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +``` + +This sets up the process to use the `batch_name` value to generate a specific filename for the final output of the workflow. + +### 3.2. Add a `batch` command-line parameter + +Now we need a way to supply the value for `batch_name` and feed it to the process call. + +#### 3.2.1. Use `params` to set up the parameter + +You already know how to use the `params` system to declare CLI parameters. +Let's use that to declare a `batch` parameter (with a default value because we are lazy). + +In the pipeline parameters section, make the following code changes: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="61" +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="61" +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' +``` + +Remember you can override that default value by specifying a value with `--batch` on the command line. + +#### 3.2.2. Pass the `batch` parameter to the process + +To provide the value of the parameter to the process, we need to add it in the process call. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="80" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect()) +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="80" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) +``` + +!!! warning + + You MUST provide the inputs to a process in the EXACT SAME ORDER as they are listed in the input definition block of the process. + +### 3.3. Run the workflow + +Let's try running this with a batch name on the command line. + +```bash +nextflow run hello-workflow.nf -resume --batch trio +``` + +It runs successfully: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-workflow.nf` [confident_rutherford] DSL2 - revision: bc58af409c + +executor > local (1) +[79/33b2f0] sayHello (2) | 3 of 3, cached: 3 ✔ +[99/79394f] convertToUpper (2) | 3 of 3, cached: 3 ✔ +[b5/f19efe] collectGreetings | 1 of 1 ✔ +``` + +And produces the desired output: + +```console title="bash" +cat results/COLLECTED-trio-output.txt +``` + +```console title="Output" +HELLO +BONJOUR +HOLà +``` + +Now, subsequent runs on other batches of inputs won't clobber previous results (as long as we specify the parameter appropriately). + +### Takeaway + +You know how to pass more than one input to a process. + +### What's next? + +Learn how to emit multiple outputs and handle them conveniently. + +--- + +## 4. Add an output to the collector step + +When a process produces only one output, it's easy to access it (in the workflow block) using the `.out` syntax. +When there are two or more outputs, the default way to select a specific output is to use the corresponding (zero-based) index; for example, you would use `.out[0]` to get the first output. +This is not terribly convenient; it's too easy to grab the wrong index. + +Let's have a look at how we can select and use a specific output of a process when there are more than one. + +For demonstration purposes, let's say we want to count and report the number of greetings that are being collected for a given batch of inputs. + +To that end, we're going to make the following refinements to the workflow: + +- Modify the process to count and output the number of greetings +- Once the process has run, select the count and report it using `view` (in the workflow block) + +### 4.1. Modify the process to count and output the number of greetings + +This will require two key changes to the process definition: we need a way to count the greetings, then we need to add that count to the `output` block of the process. + +#### 4.1.1. Count the number of greetings collected + +Conveniently, Nextflow lets us add arbitrary code in the `script:` block of the process definition, which comes in really handy for doing things like this. + +That means we can use the built-in `size()` function to get the number of files in the `input_files` array. + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="55" + script: + """ + cat ${input_files} > 'COLLECTED-${batch_id}-output.txt' + """ +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="55" + script: + count_greetings = input_files.size() + """ + cat ${input_files} > 'COLLECTED-${batch_id}-output.txt' + """ +``` + +The `count_greetings` variable will be computed at runtime. + +### 4.1.2. Emit the count as a named output + +In principle all we need to do is to add the `count_greetings` variable to the `output:` block. + +However, while we're at it, we're also going to add some `emit:` tags to our output declarations. These will enable us to select the outputs by name instead of having to use positional indices. + +In the process block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="52" + output: + path "COLLECTED-${batch_id}-output.txt" +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="52" + output: + path "COLLECTED-${batch_id}-output.txt" , emit: outfile + val count_greetings , emit: count +``` + +The `emit:` tags are optional, and we could have added a tag to only one of the outputs. +But as the saying goes, why not both? + +### 4.2. Report the output at the end of the workflow + +Now that we have two outputs coming out of the `collectGreetings` process, the `collectGreetings.out` output channel contains two 'tracks': + +- `collectGreetings.out.outfile` contains the final output file +- `collectGreetings.out.count` contains the count of greetings + +We could send either or both of these to another process for further work. However, in the interest of wrapping this up, we're just going to use `view()` to demonstrate that we can access and report the count of greetings. + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-workflow.nf" linenums="82" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) +``` + +_After:_ + +```groovy title="hello-workflow.nf" linenums="82" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } +``` + +Here we are using `$it` in the same way we did earlier, as an implicit variable to access the contents of the channel. + +!!! note + + There are a few other ways we could achieve a similar result, including some more elegant ones like the `count()` operator, but this allows us to show how to handle multiple outputs, which is what we care about. + +### 4.3. Run the workflow + +Let's try running this with the current batch of greetings. + +```bash +nextflow run hello-workflow.nf -resume --batch trio +``` + +This runs successfully: + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-workflow.nf` [evil_sinoussi] DSL2 - revision: eeca64cdb1 + +[d6/cdf466] sayHello (1) | 3 of 3, cached: 3 ✔ +[99/79394f] convertToUpper (2) | 3 of 3, cached: 3 ✔ +[9e/1dfda7] collectGreetings | 1 of 1, cached: 1 ✔ +There were 3 greetings in this batch +``` + +The last line (line 8) shows that we correctly retrieved the count of greetings processed. +Feel free to add more greetings to the CSV and see what happens. + +### Takeaway + +You know how to make a process emit a named output and how to access it from the workflow block. + +More generally, you understand the key principles involved in connecting processes together in common ways. + +### What's next? + +Take an extra long break, you've earned it. +When you're ready, move on to Part 4 to learn how to modularize your code for better maintainability and code efficiency. diff --git a/docs/hello_nextflow/04_hello_modules.md b/docs/hello_nextflow/04_hello_modules.md new file mode 100644 index 000000000..d156239b5 --- /dev/null +++ b/docs/hello_nextflow/04_hello_modules.md @@ -0,0 +1,374 @@ +# Part 4: Hello Modules + +This section covers how to organize your workflow code to make development and maintenance of your pipeline more efficient and sustainable. +Specifically, we are going to demonstrate how to use **modules**. + +In Nextflow, a **module** is a single process definition that is encapsulated by itself in a standalone code file. +To use a module in a workflow, you just add a single-line import statement to your workflow code file; then you can integrate the process into the workflow the same way you normally would. + +When we started developing our workflow, we put everything in one single code file. + +Putting processes into individual modules makes it possible to reuse process definitions in multiple workflows without producing multiple copies of the code. +This makes the code more shareable, flexible and maintainable. + +!!!note + + It is also possible to encapsulate a section of a workflow as a 'subworkflow' that can be imported into a larger pipeline, but that is outside the scope of this course. + +--- + +## 0. Warmup: Run `hello-modules.nf` + +We're going to use the workflow script `hello-modules.nf` as a starting point. +It is equivalent to the script produced by working through Part 3 of this training course. + +Just to make sure everything is working, run the script once before making any changes: + +```bash +nextflow run hello-modules.nf +``` + +```console title="Output" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-modules.nf` [festering_nobel] DSL2 - revision: eeca64cdb1 + +executor > local (7) +[25/648bdd] sayHello (2) | 3 of 3 ✔ +[60/bc6831] convertToUpper (1) | 3 of 3 ✔ +[1a/bc5901] collectGreetings | 1 of 1 ✔ +There were 3 greetings in this batch +``` + +As previously, you will find the output files in the `results` directory (specified by the `publishDir` directive). + +```console title="Directory contents" +results +├── Bonjour-output.txt +├── COLLECTED-output.txt +├── COLLECTED-test-batch-output.txt +├── COLLECTED-trio-output.txt +├── Hello-output.txt +├── Holà-output.txt +├── UPPER-Bonjour-output.txt +├── UPPER-Hello-output.txt +└── UPPER-Holà-output.txt +``` + +!!! note + + There may also be a file named `output.txt` left over if you worked through Part 2 in the same environment. + +If that worked for you, you're ready to learn how to modularize your workflow code. + +--- + +## 1. Create a directory to store modules + +It is best practice to store your modules in a specific directory. +You can call that directory anything you want, but the convention is to call it `modules/`. + +```bash +mkdir modules +``` + +!!! note + + Here we are showing how to use local modules, meaning modules stored locally in the same repository as the rest of the workflow code, in contrast to remote modules, which are stored in other (remote) repositories. For more information about remote modules, see the [documentation](https://www.nextflow.io/docs/latest/module.html). + +--- + +## 2. Create a module for `sayHello()` + +In its simplest form, turning an existing process into a module is little more than a copy-paste operation. +We're going to create a file stub for the module, copy the relevant code over then delete it from the main workflow file. + +Then all we'll need to do is add an import statement so that Nextflow will know to pull in the relevant code at runtime. + +### 2.1.1. Create a file stub for the new module + +Let's create an empty file for the module called `sayHello.nf`. + +```bash +touch modules/sayHello.nf +``` + +This gives us a place to put the process code. + +### 2.2. Move the `sayHello` process code to the module file + +Copy the whole process definition over from the workflow file to the module file, making sure to copy over the `#!/usr/bin/env nextflow` shebang too. + +```groovy title="modules/sayHello.nf" linenums="1" +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} +``` + +Once that is done, delete the process definition from the workflow file, but make sure to leave the shebang in place. + +### 2.3. Add an import declaration before the workflow block + +The syntax for importing a local module is fairly straightforward: + +```groovy title="Syntax: Import declaration" +include { } from '' +``` + +Let's insert that above the workflow block and fill it out appropriately. + +_Before:_ + +```groovy title="hello-modules.nf" linenums="50" +workflow { +``` + +_After:_ + +```groovy title="hello-modules.nf" linenums="50" +// Include modules +include { sayHello } from './modules/sayHello.nf' + +workflow { +``` + +### 2.4. Run the workflow to verify that it does the same thing as before + +We're running the workflow with essentially the same code and inputs as before, so let's run with the `-resume` flag and see what happens. + +```bash +nextflow run hello-modules.nf -resume +``` + +This runs quickly very quickly because everything is cached. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-modules.nf` [romantic_poisson] DSL2 - revision: 96edfa9ad3 + +[f6/cc0107] sayHello (1) | 3 of 3, cached: 3 ✔ +[3c/4058ba] convertToUpper (2) | 3 of 3, cached: 3 ✔ +[1a/bc5901] collectGreetings | 1 of 1, cached: 1 ✔ +There were 3 greetings in this batch +``` + +Nextflow recognized that it's still all the same work to be done, even if the code is split up into multiple files. + +### Takeaway + +You know how to extract a process into a local module and you know doing this doesn't break the resumability of the workflow. + +### What's next? + +Practice making more modules. +Once you've done one, you can do a million modules... +But let's just do two more for now. + +--- + +## 3. Modularize the `convertToUpper()` process + +### 3.1. Create a file stub for the new module + +Create an empty file for the module called `convertToUpper.nf`. + +```bash +touch modules/convertToUpper.nf +``` + +### 3.2. Move the `convertToUpper` process code to the module file + +Copy the whole process definition over from the workflow file to the module file, making sure to copy over the `#!/usr/bin/env nextflow` shebang too. + +```groovy title="modules/convertToUpper.nf" linenums="1" +#!/usr/bin/env nextflow + +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} +``` + +Once that is done, delete the process definition from the workflow file, but make sure to leave the shebang in place. + +### 3.3. Add an import declaration before the workflow block + +Insert the import declaration above the workflow block and fill it out appropriately. + +_Before:_ + +```groovy title="hello-modules.nf" linenums="31" +// Include modules +include { sayHello } from './modules/sayHello.nf' + +workflow { +``` + +_After:_ + +```groovy title="hello-modules.nf" linenums="31" +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' + +workflow { +``` + +### 3.4. Run the workflow to verify that it does the same thing as before + +Run this with the `-resume` flag. + +```bash +nextflow run hello-modules.nf -resume +``` + +This should still produce the same output as previously. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-modules.nf` [nauseous_heisenberg] DSL2 - revision: a04a9f2da0 + +[c9/763d42] sayHello (3) | 3 of 3, cached: 3 ✔ +[60/bc6831] convertToUpper (3) | 3 of 3, cached: 3 ✔ +[1a/bc5901] collectGreetings | 1 of 1, cached: 1 ✔ +There were 3 greetings in this batch +``` + +Two done, one more to go! + +--- + +## 4. Modularize the `collectGreetings()` process + +### 4.1. Create a file stub for the new module + +Create an empty file for the module called `collectGreetings.nf`. + +```bash +touch modules/collectGreetings.nf +``` + +### 4.2. Move the `collectGreetings` process code to the module file + +Copy the whole process definition over from the workflow file to the module file, making sure to copy over the `#!/usr/bin/env nextflow` shebang too. + +```groovy title="modules/collectGreetings.nf" linenums="1" +#!/usr/bin/env nextflow + +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + val batch_name + + output: + path "COLLECTED-${batch_name}-output.txt" , emit: outfile + val count_greetings , emit: count + + script: + count_greetings = input_files.size() + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +} +``` + +Once that is done, delete the process definition from the workflow file, but make sure to leave the shebang in place. + +### 4.3. Add an import declaration before the workflow block + +Insert the import declaration above the workflow block and fill it out appropriately. + +_Before:_ + +```groovy title="hello-modules.nf" linenums="9" +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' + +workflow { +``` + +_After:_ + +```groovy title="hello-modules.nf" linenums="9" +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' +include { collectGreetings } from './modules/collectGreetings.nf' + +workflow { +``` + +### 4.4. Run the workflow to verify that it does the same thing as before + +Run this with the `-resume` flag. + +```bash +nextflow run hello-modules.nf -resume +``` + +This should still produce the same output as previously. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-modules.nf` [friendly_coulomb] DSL2 - revision: 7aa2b9bc0f + +[f6/cc0107] sayHello (1) | 3 of 3, cached: 3 ✔ +[3c/4058ba] convertToUpper (2) | 3 of 3, cached: 3 ✔ +[1a/bc5901] collectGreetings | 1 of 1, cached: 1 ✔ +There were 3 greetings in this batch +``` + +### Takeaway + +You know how to modularize multiple processes in a workflow. + +Congratulations, you've done all this work and absolutely nothing has changed to how the pipeline works! + +Jokes aside, now your code is more modular, and if you decide to write another pipeline that calls on one of those processes, you just need to type one short import statement to use the relevant module. +This is better than just copy-pasting the code, because if later you decide to improve the module, all your pipelines will inherit the improvements. + +### What's next? + +Take a short break if you feel like it. +When you're ready, move on to Part 5 to learn how to use containers to manage software dependencies more conveniently and reproducibly. diff --git a/docs/hello_nextflow/05_hello_containers.md b/docs/hello_nextflow/05_hello_containers.md new file mode 100644 index 000000000..414625050 --- /dev/null +++ b/docs/hello_nextflow/05_hello_containers.md @@ -0,0 +1,649 @@ +# Part 5: Hello Containers + +In Parts 1-4 of this training course, you learned how to use the basic building blocks of Nextflow to assemble a simple workflow capable of processing some text, parallelizing execution if there were multiple inputs, and collecting the results for further processing. + +However, you were limited to basic UNIX tools available in your environment. +Real-world tasks often require various tools and packages not included by default. +Typically, you'd need to install these tools, manage their dependencies, and resolve any conflicts. + +That is all very tedious and annoying, so we're going to show you how to use **containers** to solve this problem much more conveniently. + +A **container** is a lightweight, standalone, executable unit of software created from a container **image** that includes everything needed to run an application including code, system libraries and settings. + +!!! note + + We'll be teaching this using the technology [Docker](https://www.docker.com/get-started/), but Nextflow supports [several other container technologies](https://www.nextflow.io/docs/latest/container.html#) as well. + +--- + +## 0. Warmup: Run `hello-containers.nf` + +We're going to use the workflow script `hello-containers.nf` as a starting point for the second section. +It is equivalent to the script produced by working through Part 4 of this training course. + +Just to make sure everything is working, run the script once before making any changes: + +```bash +nextflow run hello-containers.nf +``` + +This should produce the following output: + +```console title="Output" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-containers.nf` [tender_becquerel] DSL2 - revision: f7cat8e223 + +executor > local (7) +[bd/4bb541] sayHello (1) [100%] 3 of 3 ✔ +[85/b627e8] convertToUpper (3) [100%] 3 of 3 ✔ +[7d/f7961c] collectGreetings [100%] 1 of 1 ✔ +``` + +As previously, you will find the output files in the `results` directory (specified by the `publishDir` directive). + +```console title="Directory contents" +results +├── Bonjour-output.txt +├── COLLECTED-output.txt +├── COLLECTED-test-batch-output.txt +├── COLLECTED-trio-output.txt +├── Hello-output.txt +├── Holà-output.txt +├── UPPER-Bonjour-output.txt +├── UPPER-Hello-output.txt +└── UPPER-Holà-output.txt +``` + +!!! note + + There may also be a file named `output.txt` left over if you worked through Part 2 in the same environment. + +If that worked for you, you're ready to learn how to use containers. + +--- + +## 1. Use a container 'manually' + +What we want to do is add a step to our workflow that will use a container for execution. + +However, we are first going to go over some basic concepts and operations to solidify your understanding of what containers are before we start using them in Nextflow. + +### 1.1. Pull the container image + +To use a container, you usually download or "pull" a container image from a container registry, and then run the container image to create a container instance. + +The general syntax is as follows: + +```bash title="Syntax" +docker pull '' +``` + +The `docker pull` part is the instruction to the container system to pull a container image from a repository. + +The `''` part is the URI address of the container image. + +As an example, let's pull a container image that contains [cowpy](https://github.com/jeffbuttars/cowpy), a python implementation of a tool called `cowsay` that generates ASCII art to display arbitrary text inputs in a fun way. + +There are various repositories where you can find published containers. +We used the [Seqera Containers](https://seqera.io/containers/) service to generate this Docker container from the `cowpy` Conda package: `'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273'`. + +Run the complete pull command: + +```bash +docker pull 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' +``` + +This gives you the following console output as the system downloads the image: + +```console title="Output" +Unable to find image 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' locally +131d6a1b707a8e65: Pulling from library/cowpy +dafa2b0c44d2: Pull complete +dec6b097362e: Pull complete +f88da01cff0b: Pull complete +4f4fb700ef54: Pull complete +92dc97a3ef36: Pull complete +403f74b0f85e: Pull complete +10b8c00c10a5: Pull complete +17dc7ea432cc: Pull complete +bb36d6c3110d: Pull complete +0ea1a16bbe82: Pull complete +030a47592a0a: Pull complete +622dd7f15040: Pull complete +895fb5d0f4df: Pull complete +Digest: sha256:fa50498b32534d83e0a89bb21fec0c47cc03933ac95c6b6587df82aaa9d68db3 +Status: Downloaded newer image for community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273 +community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273 +``` + +Once the download is complete, you have a local copy of the container image. + +### 1.2. Use the container to run `cowpy` as a one-off command + +One very common way that people use containers is to run them directly, _i.e._ non-interactively. +This is great for running one-off commands. + +The general syntax is as follows: + +```bash title="Syntax" +docker run --rm '' [tool command] +``` + +The `docker run --rm ''` part is the instruction to the container system to spin up a container instance from a container image and execute a command in it. +The `--rm` flag tells the system to shut down the container instance after the command has completed. + +The `[tool command]` syntax depends on the tool you are using and how the container is set up. +Let's just start with `cowpy`. + +Fully assembled, the container execution command looks like this: + +```bash +docker run --rm 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' cowpy +``` + +Run it to produce the following output: + +```console title="Output" + ______________________________________________________ +< Cowacter, eyes:default, tongue:False, thoughts:False > + ------------------------------------------------------ + \ ^__^ + \ (oo)\_______ + (__)\ )\/\ + ||----w | + || || +``` + +The system spun up the container, ran the `cowpy` command with its parameters, sent the output to the console and finally, shut down the container instance. + +### 1.3. Use the container to run `cowpy` interactively + +You can also run a container interactively, which gives you a shell prompt inside the container and allows you to play with the command. + +#### 1.3.1. Spin up the container + +To run interactively, we just add `-it` to the `docker pull` command. +Optionally, we can specify the shell we want to use inside the container by appending _e.g._ `/bin/bash` to the command. + +```bash +docker run --rm -it 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' /bin/bash +``` + +Notice that your prompt changes to something like `(base) root@b645838b3314:/tmp#`, which indicates that you are now inside the container. + +You can verify this by running `ls` to list directory contents: + +```bash +ls / +``` + +```console title="Output" +bin dev etc home lib media mnt opt proc root run sbin srv sys tmp usr var +``` + +You can see that the filesystem inside the container is different from the filesystem on your host system. + +!!! note + + When you run a container, it is isolated from the host system by default. + This means that the container can't access any files on the host system unless you explicitly allow it to do so. + +You will learn how to do that in a minute. + +#### 1.3.2. Run the desired tool command(s) + +Now that you are inside the container, you can run the `cowpy` command directly and give it some parameters. +For example, the tool documentation says we can change the character ('cowacter') with `-c`. + +```bash +cowpy "Hello Containers" -c tux +``` + +Now the output shows the Linux penguin, Tux, instead of the default cow, because we specified `-c tux` parameter. + +```console title="Output" + __________________ +< Hello Containers > + ------------------ + \ + \ + .--. + |o_o | + |:_/ | + // \ \ + (| | ) + /'\_ _/`\ + \___)=(___/ +``` + +Because you're inside the container, you can run the cowpy command as many times as you like, varying the input parameters, without having to bother with Docker commands. + +!!! Tip + + Use the '-c' flag to pick a different character, including: + `beavis`, `cheese`, `daemon`, `dragonandcow`, `ghostbusters`, `kitty`, `moose`, `milk`, `stegosaurus`, `turkey`, `turtle`, `tux` + +This is neat. What would be even neater is if we could feed our `greetings.csv` as input into this. +But since we don't have access to the filesystem, we can't. + +Let's fix that. + +#### 1.3.3. Exit the container + +To exit the container, you can type `exit` at the prompt or use the ++ctrl+d++ keyboard shortcut. + +```bash +exit +``` + +Your prompt should now be back to what it was before you started the container. + +#### 1.3.4. Mount data into the container + +When you run a container, it is isolated from the host system by default. +This means that the container can't access any files on the host system unless you explicitly allow it to do so. + +One way to do this is to **mount** a **volume** from the host system into the container using the following syntax: + +```bash title="Syntax" +-v : +``` + +In our case `` will be the current working directory, so we can just use a dot (`.`), and `` is just a name we make up; let's call it `/data`. + +To mount a volume, we replace the paths and add the volume mounting argument to the docker run command as follows: + +```bash +docker run --rm -it -v .:/data 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' /bin/bash +``` + +This mounts the current working directory as a volume that will be accessible under `/data` inside the container. + +You can check that it works by listing the contents of `/data`: + +```bash +ls /data +``` + +```console title="Output" +demo-params.json hello-channels.nf hello-workflow.nf modules results +greetings.csv hello-modules.nf hello-world.nf nextflow.config work +``` + + + +You can now see the contents of the `data` directory from inside the container, including the `greetings.csv` file. + +This effectively established a tunnel through the container wall that you can use to access that part of your filesystem. + +#### 1.3.5. Use the mounted data + +Now that we have mounted the `data` directory into the container, we can use the `cowpy` command to display the contents of the `greetings.csv` file. + +To do this, we'll use `cat /data/greetings.csv | ` to pipe the contents of the CSV file into the `cowpy` command. + +```bash +cat /data/greetings.csv | cowpy -c turkey +``` + +This produces the desired ASCII art of a turkey rattling off our example greetings: + +```console title="Output" + _________ +/ HOLà \ +| HELLO | +\ BONJOUR / + --------- + \ ,+*^^*+___+++_ + \ ,*^^^^ ) + \ _+* ^**+_ + \ +^ _ _++*+_+++_, ) + _+^^*+_ ( ,+*^ ^ \+_ ) + { ) ( ,( ,_+--+--, ^) ^\ + { (\@) } f ,( ,+-^ __*_*_ ^^\_ ^\ ) + {:;-/ (_+*-+^^^^^+*+*<_ _++_)_ ) ) / + ( / ( ( ,___ ^*+_+* ) < < \ + U _/ ) *--< ) ^\-----++__) ) ) ) + ( ) _(^)^^)) ) )\^^^^^))^*+/ / / + ( / (_))_^)) ) ) ))^^^^^))^^^)__/ +^^ + ( ,/ (^))^)) ) ) ))^^^^^^^))^^) _) + *+__+* (_))^) ) ) ))^^^^^^))^^^^^)____*^ + \ \_)^)_)) ))^^^^^^^^^^))^^^^) + (_ ^\__^^^^^^^^^^^^))^^^^^^^) + ^\___ ^\__^^^^^^))^^^^^^^^)\\ + ^^^^^\uuu/^^\uuu/^^^^\^\^\^\^\^\^\^\ + ___) >____) >___ ^\_\_\_\_\_\_\) + ^^^//\\_^^//\\_^ ^(\_\_\_\) + ^^^ ^^ ^^^ ^ +``` + +Feel free to play around with this command. +When you're done, exit the container as previously: + +```bash +exit +``` + +You will find yourself back in your normal shell. + +### Takeaway + +You know how to pull a container and run it either as a one-off or interactively. You also know how to make your data accessible from within your container, which lets you try any tool you're interested in on real data without having to install any software on your system. + +### What's next? + +Learn how to use containers for the execution of Nextflow processes. + +--- + +## 2. Use containers in Nextflow + +Nextflow has built-in support for running processes inside containers to let you run tools you don't have installed in your compute environment. +This means that you can use any container image you like to run your processes, and Nextflow will take care of pulling the image, mounting the data, and running the process inside it. + +To demonstrate this, we are going to add a `cowpy` step to the pipeline we've been developing, after the `collectGreetings` step. + +### 2.1. Write a `cowpy` module + +#### 2.1.1. Create a file stub for the new module + +Create an empty file for the module called `cowpy.nf`. + +```bash +touch modules/cowpy.nf +``` + +This gives us a place to put the process code. + +#### 2.1.2. Copy the `cowpy` process code in the module file + +We can model our `cowpy` process on the other processes we've written previously. + +```groovy title="modules/cowpy.nf" linenums="1" +#!/usr/bin/env nextflow + +// Generate ASCII art with cowpy +process cowpy { + + publishDir 'results', mode: 'copy' + + input: + path input_file + val character + + output: + path "cowpy-${input_file}" + + script: + """ + cat $input_file | cowpy -c "$character" > cowpy-${input_file} + """ + +} +``` + +The output will be a new text file containing the ASCII art generated by the `cowpy` tool. + +### 2.2. Add cowpy to the workflow + +Now we need to import the module and call the process. + +#### 2.2.1. Import the `cowpy` process into `hello-containers.nf` + +Insert the import declaration above the workflow block and fill it out appropriately. + +_Before:_ + +```groovy title="hello-containers.nf" linenums="9" +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' +include { collectGreetings } from './modules/collectGreetings.nf' + +workflow { +``` + +_After:_ + +```groovy title="hello-containers.nf" linenums="9" +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' +include { collectGreetings } from './modules/collectGreetings.nf' +include { cowpy } from './modules/cowpy.nf' + +workflow { +``` + +#### 2.2.2. Add a call to the `cowpy` process in the workflow + +Let's connect the `cowpy()` process to the output of the `collectGreetings()` process, which as you may recall produces two outputs: + +- `collectGreetings.out.outfile` contains the output file +- `collectGreetings.out.count` contains the count of greetings per batch + +In the workflow block, make the following code change: + +_Before:_ + +```groovy title="hello-containers.nf" linenums="28" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view{ "There were $it greetings in this batch" } +``` + +_After:_ + +```groovy title="hello-containers.nf" linenums="28" + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view{ "There were $it greetings in this batch" } + + // generate ASCII art of the greetings with cowpy + cowpy(collectGreetings.out.outfile, params.character) +``` + +Notice that we include a new CLI parameter, `params.character`, in order to specify which character we want to have say the greetings. + +#### 2.2.3. Set a default value for `params.character` + +We like to be lazy and skip typing parameters in our command lines. + +_Before:_ + +```groovy title="hello-containers.nf" linenums="3" +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' +``` + +_After:_ + +```groovy title="hello-containers.nf" linenums="3" +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' +params.character = 'turkey' +``` + +That should be all we need to make this work. + +#### 2.2.4. Run the workflow to verify that it works + +Run this with the `-resume` flag. + +```bash +nextflow run hello-containers.nf -resume +``` + +Oh no, there's an error! + +```console title="Output" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-containers.nf` [special_lovelace] DSL2 - revision: 028a841db1 + +executor > local (1) +[f6/cc0107] sayHello (1) | 3 of 3, cached: 3 ✔ +[2c/67a06b] convertToUpper (3) | 3 of 3, cached: 3 ✔ +[1a/bc5901] collectGreetings | 1 of 1, cached: 1 ✔ +[b2/488871] cowpy | 0 of 1 +There were 3 greetings in this batch +ERROR ~ Error executing process > 'cowpy' + +Caused by: + Process `cowpy` terminated with an error exit status (127) +``` + +This error code, `error exit status (127)` means the executable we asked for was not found. + +Of course, since we're calling the `cowpy` tool but we haven't actually specified a container yet. + +### 2.3. Use a container to run it + +We need to specify a container and tell Nextflow to use it for the `cowpy()` process. + +#### 2.3.1. Specify a container for the `cowpy` process to use + +Edit the `cowpy.nf` module to add the `container` directive to the process definition as follows: + +_Before:_ + +```groovy title="modules/cowpy.nf" linenums="4" +process cowpy { + + publishDir 'containers/results', mode: 'copy' +``` + +_After:_ + +```groovy title="modules/cowpy.nf" linenums="4" +process cowpy { + + publishDir 'containers/results', mode: 'copy' + + container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' +``` + +This tells Nextflow that if the use of Docker is enabled, it should use the container image specified here to execute the process. + +#### 2.3.2. Enable use of Docker via the `nextflow.config` file + +Here we are going to slightly anticipate the topic of the next and last part of this course (Part 6), which covers configuration. + +One of the main ways Nextflow offers for configuring workflow execution is to use a `nextflow.config` file. When such a file is present in the current directory, Nextflow will automatically load it in and apply any configuration it contains. + +We provided a `nextflow.config` file with a single line of code that disables Docker: `docker.enabled = false`. + +Now, let's switch that to `true` to enable Docker: + +_Before:_ + +```console title="nextflow.config" linenums="1" +docker.enabled = false +``` + +_After:_ + +```console title="nextflow.config" linenums="1" +docker.enabled = true +``` + +!!! note + + It is possible to enable Docker execution from the command-line, on a per-run basis, using the `-with-docker ` parameter. + However, that only allows us to specify one container for the entire workflow, whereas the approach we just showed you allows us to specify a different container per process. + This is better for modularity, code maintenance and reproducibility. + +#### 2.3.3. Run the workflow with Docker enabled + +Run the workflow with the `-resume` flag: + +```bash +nextflow run hello-containers.nf -resume +``` + +This time it does indeed work. + +```console title="Output" linenums="1" + N E X T F L O W ~ version 24.10.0 + +Launching `hello-containers.nf` [elegant_brattain] DSL2 - revision: 028a841db1 + +executor > local (1) +[95/fa0bac] sayHello (3) | 3 of 3, cached: 3 ✔ +[92/32533f] convertToUpper (3) | 3 of 3, cached: 3 ✔ +[aa/e697a2] collectGreetings | 1 of 1, cached: 1 ✔ +[7f/caf718] cowpy | 1 of 1 ✔ +There were 3 greetings in this batch +``` + +You can find the cowpy'ed output in the `results` directory. + +```console title="results/cowpy-COLLECTED-test-batch-output.txt" + _______ + / \ +| HELLO | +| HOLà | +| BONJOUR | + \ / + ======= + \ + \ + \ + \ + ,. + (_|,. + ,' /, )_______ _ + __j o``-' `.'-)' + (") \' + `-j | + `-._( / + |_\ |--^. / + /_]'|_| /_)_/ + /_]' /_]' +``` + +You see that the character is saying all the greetings, just as it did when we ran the `cowpy` command on the `greetings.csv` file from inside the container. + + + +#### 2.3.4. Inspect how Nextflow launched the containerized task + +Let's take a look at the work subdirectory for one of the `cowpy` process calls to get a bit more insight on how Nextflow works with containers under the hood. + +Check the output from your `nextflow run` command to find the call ID for the `cowpy` process. +Then navigate to the work subdirectory. +In it, you will find the `.command.run` file that contains all the commands Nextflow ran on your behalf in the course of executing the pipeline. + +Open the `.command.run` file and search for `nxf_launch`; you should see something like this: + +```bash +nxf_launch() { + docker run -i --cpu-shares 1024 -e "NXF_TASK_WORKDIR" -v /workspace/gitpod/hello-nextflow/work:/workspace/gitpod/hello-nextflow/work -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID community.wave.seqera.io/library/pip_cowpy:131d6a1b707a8e65 /bin/bash -ue /workspace/gitpod/hello-nextflow/work/7f/caf7189fca6c56ba627b75749edcb3/.command.sh +} +``` + +As you can see, Nextflow is using the `docker run` command to launch the process call. +It also mounts the corresponding work subdirectory into the container, sets the working directory inside the container accordingly, and runs our templated bash script in the `.command.sh` file. + +All the hard work we had to do manually in the previous section is done for us by Nextflow! + +### Takeaway + +You know how to use containers in Nextflow to run processes. + +### What's next? + +Take a break! +When you're ready, move on to Part 6 to learn how to configure the execution of your pipeline to fit your infrastructure as well as manage configuration of inputs and parameters. +It's the very last part and then you're done! diff --git a/docs/hello_nextflow/06_hello_config.md b/docs/hello_nextflow/06_hello_config.md index a780aaef4..24791db1a 100644 --- a/docs/hello_nextflow/06_hello_config.md +++ b/docs/hello_nextflow/06_hello_config.md @@ -1,341 +1,161 @@ -# Part 5: Hello Config +# Part 6: Hello Config This section will explore how to set up and manage the configuration of your Nextflow pipeline so that you'll be able to customize its behavior, adapt it to different environments, and optimize resource usage _without altering a single line of the workflow code itself_. -We're going to cover essential components of Nextflow configuration such as config files, profiles, process directives, executors, and parameter files. -By learning to utilize these configuration options effectively, you can enhance the flexibility, scalability, and performance of your pipelines. - ---- - -## 0. Warmup: Moving to a formal project structure - -So far we've been working with a very loose structure, with just one workflow code file and a tiny configuration file that we've mostly ignored, because we were very focused on learning how to implement the workflow itself. -However, we're now moving into the phase of this training series that is more focused on code development and maintenance practices. - -As part of that, we're going to adopt a formal project structure. -We're going to work inside a dedicated project directory called `hello-config`, and we've renamed the workflow file `main.nf` to match the recommended Nextflow convention. - -### 0.1. Explore the `hello-config` directory - -We want to launch the workflow from inside the `hello-config` directory, so let's move into it now. - -```bash -cd hello-config -``` - -Let's take a look at the contents. -You can use the file explorer or the terminal; here we're using the output of `tree` to display the top-level directory contents. - -```console title="Directory contents" -hello-config -├── demo-params.json -├── main.nf -└── nextflow.config -``` - -- **`main.nf`** is a workflow based on `hello-operators.nf`, the workflow produced by completing Part 4 of this training course; - -- **`nextflow.config`** is a copy of the original `nextflow.config` file from the `hello-nextflow` directory, one level up (where we've been working so far). - Whenever there is a file named `nextflow.config` in the current directory, Nextflow will automatically load configuration from it. The one we have been using contains the following lines: - - ```console title="nextflow.config" linenums="1" - docker.fixOwnership = true - docker.enabled = true - ``` - - The `docker.fixOwnership = true` line is not really interesting. - It's a workaround for an issue that sometimes occur with containerized tools that set the wrong permissions on the files they write (which is the case with GenomicsDBImport in the GATK container image in our workflow). - - The `docker.enabled = true` line is what we care about here. - It specifies that Nextflow should use Docker to run process calls that specify a container image. - We're going to be playing with that shortly. +There are multiple ways to do this; here we are going to use the simplest and most common configuration file mechanism, the `nextflow.config` file. +Whenever there is a file named `nextflow.config` in the current directory, Nextflow will automatically load configuration from it. !!!note Anything you put into the `nextflow.config` can be overridden at runtime by providing the relevant process directives or parameters and values on the command line, or by importing another configuration file, according to the order of precedence described [here](https://www.nextflow.io/docs/latest/config.html). -- **`demo-params.json`** is a parameter file intended for supplying parameter values to a workflow. - We will use it in section 5 of this tutorial. - -The one thing that's missing is a way to point to the original data without making a copy of it or updating the file paths wherever they're specified. -The simplest solution is to link to the data location. - -### 0.2. Create a symbolic link to the data - -Run this command from inside the `hello-config` directory: - -```bash -ln -s ../data data -``` - -This creates a symbolic link called `data` pointing to the data directory, which allows us to avoid having to change anything to how the file paths are set up. - -```console title="Directory contents" -hello-config -├── data -> ../data -├── demo-params.json -├── main.nf -└── nextflow.config -``` - -Later we'll cover a better way of handling this, but this will do for now. +In this part of the training, we're going to use the `nextflow.config` file to demonstrate essential components of Nextflow configuration such as process directives, executors, profiles, and parameter files. -### 0.3. Verify that the initial workflow runs properly - -Now that everything is in place, we should be able to run the workflow successfully. - -```bash -nextflow run main.nf -``` - -This should run successfully: - -```console title="Output" -Nextflow 24.09.2-edge is available - Please consider updating your version to it - - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `main.nf` [tender_brahmagupta] DSL2 - revision: 848ff2f9b5 - -executor > local (7) -[fb/f755b1] SAMTOOLS_INDEX (1) [100%] 3 of 3 ✔ -[d8/467767] GATK_HAPLOTYPECALLER (1) [100%] 3 of 3 ✔ -[ee/2c7855] GATK_JOINTGENOTYPING [100%] 1 of 1 ✔ -``` - -There will now be a `work` directory and a `results_genomics` directory inside your `hello-config` directory. - -### Takeaway - -You know what are the two most important files in a Nextflow project: `main.nf` and its `nextflow.config`. - -### What's next? - -Learn how to modify basic configuration properties to adapt to your compute environment's requirements. +By learning to utilize these configuration options effectively, you can enhance the flexibility, scalability, and performance of your pipelines. --- -## 1. Determine what software packaging technology to use - -In the very first part of this training course (Part 1: Hello World) we just used locally installed software in our workflow. Then from Part 2 onward, we've been using Docker containers. - -Now, let's pretend we're working on an HPC cluster and the admin doesn't allow the use of Docker for security reasons. +## 0. Warmup: Check that Docker is enabled and run the Hello Config workflow -### 1.1. Disable Docker in the config file +First, a quick check. There is a `nextflow.config` file in the current directory that contains the line `docker.enabled = `, where `` is either `true` or `false` depending on whether or not you've worked through Part 5 of this course in the same environment. -First, we have to switch the value of `docker.enabled` to false. +If it is set to `true`, you don't need to do anything. -_Before:_ +If it is set to `false`, switch it to `true` now. ```console title="nextflow.config" linenums="1" -docker.fixOwnership = true docker.enabled = true ``` -_After:_ - -```console title="nextflow.config" linenums="1" -docker.fixOwnership = true -docker.enabled = false -``` - -Let's see what happens if we run that. - -### 1.2. Run the workflow without Docker - -We are now launching the `main.nf` workflow from inside the `hello-config` directory. +Once you've done that, verify that the initial workflow runs properly: ```bash -nextflow run main.nf +nextflow run hello-config.nf ``` -As expected, the run fails with an error message that looks like this: - ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `hello-config/main.nf` [silly_ramanujan] DSL2 - revision: 9129bc4618 +Launching `hello-config.nf` [reverent_heisenberg] DSL2 - revision: 028a841db1 + +executor > local (8) +[7f/0da515] sayHello (1) | 3 of 3 ✔ +[f3/42f5a5] convertToUpper (3) | 3 of 3 ✔ +[04/fe90e4] collectGreetings | 1 of 1 ✔ +[81/4f5fa9] cowpy | 1 of 1 ✔ +There were 3 greetings in this batch +``` -executor > local (3) -[93/4417d0] SAMTOOLS_INDEX (1) [ 0%] 0 of 3 -[- ] GATK_HAPLOTYPECALLER - -[- ] GATK_JOINTGENOTYPING - -ERROR ~ Error executing process > 'SAMTOOLS_INDEX (2)' +If everything works, you're ready to learn how to modify basic configuration properties to adapt to your compute environment's requirements. -Caused by: - Process `SAMTOOLS_INDEX (2)` terminated with an error exit status (127) +--- -Command executed: +## 1. Determine what software packaging technology to use - samtools index 'reads_father.bam' +The first step toward adapting your workflow configuration to your compute environment is specifying where the software packages that will get run in each step are going to be coming from. +Are they already installed in the local compute environment? Do we need to retrieve images and run them via a container system? Or do we need to retrieve Conda packages and build a local Conda environment? -Command exit status: - 127 +In the very first part of this training course (Parts 1-4) we just used locally installed software in our workflow. +Then in Part 5, we introduced Docker containers and the `nextflow.config` file, which we used to enable the use of Docker containers. -Command output: - (empty) +In the warmup to this section, you checked that Docker was enabled in `nextflow.config` file and ran the workflow, which used a Docker container to execute the `cowpy()` process. -Command error: - .command.sh: line 2: samtools: command not found -``` +!!! note -Command not found? Of course, we don't have Samtools installed in our environment, and we can no longer use the Docker container. What to do? + If that doesn't sound familiar, you should probably go back and work through Part 5 before continuing. -!!!note +Now let's see how we can configure an alternative software packaging option via the `nextflow.config` file. - Nextflow supports multiple other container technologies such as including Singularity (which is more widely used on HPC), and software package managers such as Conda. +### 1.1. Disable Docker and enable Conda in the config file -Let's try using Conda environments for our workflow. +Let's pretend we're working on an HPC cluster and the admin doesn't allow the use of Docker for security reasons. -### 1.3. Enable Conda in the configuration file +Fortunately for us, Nextflow supports multiple other container technologies such as including Singularity (which is more widely used on HPC), and software package managers such as Conda. -First, we need to add a directive enabling the use of Conda, right after the line that controls the use of Docker. -And while we're at it, let's put a blank line before those two to emphasize the logical grouping. +We can change our configuration file to use Conda instead of Docker. +To do so, we switch the value of `docker.enabled` to `false`, and add a directive enabling the use of Conda: _Before:_ ```groovy title="nextflow.config" linenums="1" -docker.fixOwnership = true -docker.enabled = false +docker.enabled = true ``` _After:_ ```groovy title="nextflow.config" linenums="1" -docker.fixOwnership = true - docker.enabled = false conda.enabled = true ``` -This should allow Nextflow to create and utilize Conda environments for processes that have Conda packages specified. Which means we now need to add those to our processes! +This will allow Nextflow to create and utilize Conda environments for processes that have Conda packages specified. +Which means we now need to add one of those to our `cowpy` process! -### 1.4. Specify Conda packages in the process definitions +### 1.2. Specify a Conda package in the process definition -We know that the Bioconda project provides Conda packages for Samtools and GATK, so we just need to retrieve their URIs and add them to the corresponding process definitions using the `conda` directive. +We've already retrieved the URI for a Conda package containing the `cowpy` tool: `conda-forge::cowpy==1.1.5` !!! note There are a few different ways to get the URI for a given conda package. - We recommend using the [Seqera Containers](https://seqera.io/containers/) search query, which will give you a URI that you can copy paste, even if you're not creating a container. - -For your convenience, we are providing the URIs below. Just make sure to _add_ the `conda` directive. -To be clear, we're not _replacing_ the `docker` directive, just adding an alternative option. - -#### 1.4.1. Update SAMTOOLS_INDEX - -The URI is `"bioconda::samtools=1.20"`. - -_Before:_ - -```console title="main.nf" linenums="22" -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' -``` - -_After:_ - -```console title="main.nf" linenums="22" -process SAMTOOLS_INDEX { - - container "community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464" - conda "bioconda::samtools=1.20" + We recommend using the [Seqera Containers](https://seqera.io/containers/) search query, which will give you a URI that you can copy and paste, even if you're not planning to create a container from it. - publishDir params.outdir, mode: 'symlink' -``` - -#### 1.4.2. Update GATK_HAPLOTYPECALLER - -The URI is `"bioconda::gatk4=4.5.0.0"`. - -_Before:_ - -```console title="main.nf" linenums="43" -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' -``` - -_After:_ - -```console title="main.nf" linenums="43" -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' -``` - -#### 1.4.3. Update GATK_JOINTGENOTYPING - -The URI is `"bioconda::gatk4=4.5.0.0"`. +Now we add the URI to the `cowpy` process definition using the `conda` directive: _Before:_ -```console title="main.nf" linenums="74" -process GATK_JOINTGENOTYPING { +```console title="modules/cowpy.nf" linenums="4" +process cowpy { - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" + container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' - publishDir params.outdir, mode: 'symlink' + publishDir 'results', mode: 'copy' ``` _After:_ -```console title="main.nf" linenums="74" -process GATK_JOINTGENOTYPING { +```console title="modules/cowpy.nf" linenums="4" +process cowpy { - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" + container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' + conda 'conda-forge::cowpy==1.1.5' - publishDir params.outdir, mode: 'symlink' + publishDir 'results', mode: 'copy' ``` -Once all three processes are updated, we can try running the workflow again. +To be clear, we're not _replacing_ the `docker` directive, we're _adding_ an alternative option. -### 1.5. Run the workflow to verify that it can use Conda +### 1.3. Run the workflow to verify that it can use Conda Let's try it out. ```bash -nextflow run main.nf +nextflow run hello-config.nf ``` -This will take a bit longer than usual the first time, and you might see the console output stay 'stuck' at this stage for a minute or so: +This should work without issue. ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `main.nf` [extravagant_thompson] DSL2 - revision: 848ff2f9b5 +Launching `hello-config.nf` [trusting_lovelace] DSL2 - revision: 028a841db1 -[- ] SAMTOOLS_INDEX - -[- ] GATK_HAPLOTYPECALLER - -[- ] GATK_JOINTGENOTYPING - -Creating env using conda: bioconda::samtools=1.20 [cache /workspace/gitpod/hello-nextflow/hello-config/work/conda/env-6684ea23d69ceb1742019ff36904f612] +executor > local (8) +[ee/4ca1f2] sayHello (3) | 3 of 3 ✔ +[20/2596a7] convertToUpper (1) | 3 of 3 ✔ +[b3/e15de5] collectGreetings | 1 of 1 ✔ +[c5/af5f88] cowpy | 1 of 1 ✔ +There were 3 greetings in this batch ``` -That's because Nextflow has to retrieve the Conda packages and create the environment, which takes a bit of work behind the scenes. The good news is that you don't need to deal with any of it yourself! - -After a few moments, it should spit out some more output, and eventually complete without error. - -```console title="Output" - N E X T F L O W ~ version 24.10.0 +Behind the scenes, Nextflow has retrieved the Conda packages and created the environment, which normally takes a bit of work; so it's nice that we don't have to do any of that ourselves! - ┃ Launching `main.nf` [silly_goldstine] DSL2 - revision: a60f9fd6af +!!! note -executor > local (7) -[23/b59106] SAMTOOLS_INDEX (1) [100%] 3 of 3 ✔ -[da/e1bf1d] GATK_HAPLOTYPECALLER (1) [100%] 3 of 3 ✔ -[2e/e6ffca] GATK_JOINTGENOTYPING [100%] 1 of 1 ✔ -``` + This runs quickly because the `cowpy` package is quite small, but if you're working with large packages, it may take a bit longer than usual the first time, and you might see the console output stay 'stuck' for a minute or so before completing. + This is normal and is due to the extra work Nextflow does the first time you use a new package. -And from our standpoint, it looks like it works exactly the same as running with Docker, even though on the backend the mechanics are a bit different. +From our standpoint, it looks like it works exactly the same as running with Docker, even though on the backend the mechanics are a bit different. This means we're all set to run with Conda environments if needed. @@ -353,432 +173,103 @@ You know how to configure which software package each process should use, and ho ### What's next? -Learn how to use profiles to make selecting an option easier. - ---- - -## 2. Use profiles to select preset configurations - -Profiles are a great way to adapt your workflow configuration by selecting preset options at runtime, to avoid having to edit a file every time you want to run something differently. - -### 2.1. Create profiles for switching between Docker and Conda - -Setting up these profiles mainly involves restructuring how we specify the `docker` and `conda` directives. - -_Before:_ - -```groovy title="nextflow.config" linenums="1" -docker.fixOwnership = true - -docker.enabled = false -conda.enabled = true -``` - -_After:_ - -```groovy title="nextflow.config" linenums="1" -docker.fixOwnership = true - -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } -} -``` - -This makes it possible to activate one or the other by specifying a profile in our Nextflow run command line. - -### 2.2. Run the workflow with a profile - -Let's try running the workflow with Conda. - -```bash -nextflow run main.nf -profile conda_on -``` - -It works! Convenient, isn't it? - -``` - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `main.nf` [sharp_gauss] DSL2 - revision: 66cd7c255a - -executor > local (7) -[f4/ef2cb6] SAMTOOLS_INDEX (1) [100%] 3 of 3 ✔ -[70/77152c] GATK_HAPLOTYPECALLER (1) [100%] 3 of 3 ✔ -[a6/0f72fd] GATK_JOINTGENOTYPING [100%] 1 of 1 ✔ -``` - -Feel free to try it out with the Docker profile too. You just have to switch `-profile conda_on` to `-profile docker_on` in the command. - -### Takeaway - -You know how to use profiles to select a preset configuration at runtime with minimal hassle. - -### What's next? - Learn how to change the executor used by Nextflow to actually do the work. --- -## 3. Determine what executor(s) should be used to do the work - -Until now, we have been running our pipeline with the local executor. -This runs each step on the same machine that Nextflow is running on. -However, for large workloads, you will typically want to use a distributed executor such as an HPC or cloud. -Nextflow supports several different distributed executors, including: +## 2. Allocate compute resources with process directives -- HPC (SLURM, PBS, SGE) -- AWS Batch -- Google Batch -- Azure Batch -- Kubernetes -- GA4GH TES +Most high-performance computing platforms allow (and sometimes require) that you specify certain resource allocation parameters such as number of CPUs and memory. -The executor is subject to a process directive called `executor`. By default it is set to `local`, so the following configuration is implied: +By default, Nextflow will use a single CPU and 2GB of memory for each process. +The corresponding process directives are called `cpus` and `memory`, so the following configuration is implied: -```groovy title="Built-in configuration" +```groovy title="Built-in configuration" linenums="1" process { - executor = 'local' + cpus = 1 + memory = 2.GB } ``` -Let's look at what it would take to using a Slurm scheduler, assuming we had a connection to a cluster and Slurm was installed appropriately. - -!!! warning - - What follows is for demonstration purposes but **will not execute the work** since we don't have access to an external executor. - -### 3.1. Set up a Slurm executor - -Add the following lines to the `nextflow.config` file: +You can modify these values, either for all processes or for specific named processes, using additional process directives in your configuration file. +Nextflow will translate them into the appropriate instructions for the chosen executor. -```groovy title="nextflow.config" linenums="12" -process { - executor = 'slurm' -} -``` +But how do you know what values to use? -And... that's it! As noted before, this does assume that Slurm itself is already set up for you, but this is really all Nextflow itself needs to know. +### 2.1. Run the workflow to generate a resource utilization report -Basically we are telling Nextflow to generate a Slurm submission script and submit it using an `sbatch` command. +If you don't know up front how much CPU and memory your processes are likely to need, you can do some resource profiling, meaning you run the workflow with some default allocations, record how much each process used, and from there, estimate how to adjust the base allocations. -### 3.2. Launch the workflow to generate the job submission script +Conveniently, Nextflow includes built-in tools for doing this, and will happily generate a report for you on request. -Let's try running this; even though we know it won't execute (since we don't have Slurm set up in this Gitpod environment) we'll be able to see what the submission script looks like. +To do so, add `-with-report .html` to your command line. ```bash -nextflow run main.nf -profile conda_on -``` - -As expected, this fails with a fairly unambiguous error: - -```console title="Output" -nextflow - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `main.nf` [grave_gauss] DSL2 - revision: 66cd7c255a - -[- ] SAMTOOLS_INDEX [ 0%] 0 of 3 -[eb/2962ce] SAMTOOLS_INDEX (3) [ 33%] 1 of 3, failed: 1 -[- ] GATK_HAPLOTYPECALLER - -[- ] GATK_JOINTGENOTYPING - -ERROR ~ Error executing process > 'SAMTOOLS_INDEX (3)' - -Caused by: - java.io.IOException: Cannot run program "sbatch" (in directory "/workspace/gitpod/hello-nextflow/hello-config/work/eb/2962ce167b3025a41ece6ce6d7efc2"): error=2, No such file or directory - -Command executed: - - sbatch .command.run -``` - -However, it did produce what we are looking for: the `.command.run` file that Nextflow tried to submit to Slurm via the `sbatch` command. - -Let's take a look inside. - -```bash title=".command.run" linenums="1" -#!/bin/bash -#SBATCH -J nf-SAMTOOLS_INDEX_(1) -#SBATCH -o /home/gitpod/work/34/850fe31af0eb62a0eb1643ed77b84f/.command.log -#SBATCH --no-requeue -#SBATCH --signal B:USR2@30 -NXF_CHDIR=/home/gitpod/work/34/850fe31af0eb62a0eb1643ed77b84f -### --- -### name: 'SAMTOOLS_INDEX (1)' -### container: 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' -### outputs: -### - 'reads_father.bam' -### - 'reads_father.bam.bai' -### ... +nextflow run hello-config.nf -with-report report-config-1.html ``` -This shows the job submission details that Nextflow is trying to hand over to Slurm. - -!!!note - - There other options that we could additionally set using other process directives to control resource allocations, which we'll get to in a little bit. - These would also be included in the `.command.run` file and directly passed to the Slurm execution. +The report is an html file, which you can download and open in your browser. You can also right click it in the file explorer on the left and click on `Show preview` in order to view it in the training environment. -You can try using any of the other supported executors in the same way. Nextflow will translate the values submitted to the executor into the appropriate equivalent instructions. - -Conveniently, you can also set up profiles to select which executor you want to use at runtime, just like we did for the Docker vs. Conda environments selection earlier. +Take a few minutes to look through the report and see if you can identify some opportunities for adjusting resources. +Make sure to click on the tabs that show the utilization results as a percentage of what was allocated. +There is some [documentation](https://www.nextflow.io/docs/latest/reports.html) describing all the available features. -### 3.3. Set up profiles for executors too + -Let's replace the process block we had added with the executor selection profiles. +### 2.2. Set resource allocations for all processes -_Before:_ +The profiling shows that the processes in our training workflow are very lightweight, so let's reduce the default memory allocation to 1GB per process. -```groovy title="nextflow.config" linenums="3" -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } -} +Add the following to your `nextflow.config` file: +```groovy title="nextflow.config" linenums="4" process { - executor = 'slurm' -} -``` - -_After:_ - -```groovy title="nextflow.config" linenums="3" -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - local_exec { - process.executor = 'local' - } - slurm_exec { - process.executor = 'slurm' - } + memory = 1.GB } ``` -Although it may look like these are going to be mutually exclusive, you can actually combine multiple profiles. -Let's try that now. - -### 3.4. Run with a combination of profiles - -To use two profiles at the same time, simply give both to the `-profile` parameter, separated by a comma. - -```bash -nextflow run main.nf -profile docker_on,local_exec -``` - -With that, we've returned to the original configuration of using Docker containers with local execution, not that you can tell from the console output: +### 2.3. Set resource allocations for an individual process -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `main.nf` [irreverent_bassi] DSL2 - revision: 66cd7c255a - -executor > local (7) -[17/82bbc4] SAMTOOLS_INDEX (2) [100%] 3 of 3 ✔ -[8e/93609c] GATK_HAPLOTYPECALLER (2) [100%] 3 of 3 ✔ -[e6/df6740] GATK_JOINTGENOTYPING [100%] 1 of 1 ✔ -``` - -The point is, we can now use profiles to switch to a different software packaging system (Conda) or a different executor (such as Slurm) with a single command-line option. -For example, if we were back on our hypothetical HPC from earlier, we would switch to using `-profile conda_on,slurm_exec` in our Nextflow command line. - -Feel free to test that on your own to satisfy yourself that it works as expected. - -Moving on, we're going to take this logic a step further, and set up dedicated profiles for groups of configuration elements that we usually want to activate together. - -### 3.5. Create profiles that combine several configuration elements - -Let's set up some dedicated profiles for the two case figures we've been envisioning: running locally with Docker, which we'll call `my_laptop`, and running on the HPC cluster with Conda, which we'll call `univ_hpc`. +At the same time, we're going to pretend that the `cowpy` process requires more resources than the others, just so we can demonstrate how to adjust allocations for an individual process. _Before:_ -```groovy title="nextflow.config" linenums="3" -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - local_exec { - process.executor = 'local' - } - slurm_exec { - process.executor = 'slurm' - } -} -``` - -_After:_ - -```groovy title="nextflow.config" linenums="3" -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - my_laptop { - process.executor = 'local' - docker.enabled = true - } - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - } -} -``` - -Now we have profiles for the two main case figures we've been considering. -If in the future we find other elements of configuration that are always co-occurring with these, we can simply add them to the corresponding profile(s). - -Feel free to test these new profiles on your own using either `-profile my_laptop` or `-profile univ_hpc`. -Just remember that the `univ_hpc` one won't work unless you run it in an environment that is set up appropriately to use Slurm. - -!!!note - - You'll notice we've removed the two profiles that _only_ specified the executor, because in those cases we're always going to want to specify the software packaging technology too. - - We're leaving in the Docker and Conda profiles because those ones come in handy by themselves, although there are also some dedicated command line flags for those, and it's a nice illustration of the fact that you can have the same directives set in multiple profiles. - Just keep in mind that if you combine profiles with conflicting settings for the same directives, you might be surprised by the results. - -### Takeaway - -You now know how to change the executor and combine that with other environment settings using profiles. - -### What's next? - -Learn how to control the resources allocated for executing processes. - ---- - -## 4. Allocate compute resources with process directives - -We've covered how to control what compute environment Nextflow is going to use to run the workflow, so now the next logical question is, how do we control the resources (CPU, memory etc) that will be allocated? - -The answer may not surprise you; it's process directives again. - -### 4.1. Increase default process resource allocations - -By default, Nextflow will use a single CPU and 2GB of memory for each process. -Let's say we decide to double that. - -We can modify this behavior by setting the `cpu` and `memory` directives in the `process` block. Add the following to the end of your `nextflow.config` file: - -```groovy title="nextflow.config" linenums="20" +```groovy title="nextflow.config" linenums="14" process { - // defaults for all processes - cpus = 2 - memory = 4.GB + memory = 1.GB } ``` -### 4.2. Run the workflow with the increased defaults - -Let's try that out, bearing in mind that we need to keep `-profile my_laptop` in the command going forward. - -```bash -nextflow run main.nf -profile my_laptop -``` - -You may not notice any real difference in how quickly this runs, since this is such a small workload. -But if you have a machine with few CPUs and you allocate a high number per process, you might see process calls getting queued behind each other. -This is because Nextflow will ensure we aren't using more CPUs than are available. - -!!! tip - - You can check the number of CPUs allocated to a given process by looking at the `.command.run` log in its work directory. - There will be a function called `nxf_launch()` that includes the command `docker run—i—-CPU 1024`, where `--cpu-shares` refers to the CPU time given to this process' tasks. Setting one task's cpu_share to 512 and another to 1024 means that the second task will get double the amount of CPU time as the first. - -You're probably wondering if you can set resource allocations per individual process, and the answer is of course yes, yes you can! -We'll show you how to do that in a moment. - -But first, let's talk about how you can find out how much CPU and memory your processes are likely to need. -The classic approach is to do resource profiling, meaning you run the workflow with some default allocations, record how much each process used, and from there, estimate how to adjust the base allocations. - -The truly excellent news on this front is that Nextflow includes built-in tools for doing this, and will happily generate a report for you on request. -Let's try that out. - -### 4.3. Run the workflow to generate a resource utilization report - -To have Nextflow generate the report automatically, simply add `-with-report .html` to your command line. - -```bash -nextflow run main.nf -profile my_laptop -with-report report-config-1.html -``` - -The report is an html file, which you can download and open in your browser. You can also right click it in the file explorer on the left and click on `Show preview` in order to view it on Gitpod. - -Take a few minutes to look through the report and see if you can identify some opportunities for adjusting resources. -Make sure to click on the tabs that show the utilization results as a percentage of what was allocated. -There is some [documentation](https://www.nextflow.io/docs/latest/reports.html) describing all the available features. - - - -One observation is that the `GATK_JOINTGENOTYPING` seems to be very hungry for CPU, which makes sense since it performs a lot of complex calculations. -So we could try boosting that and see if it cuts down on runtime. - -However, we seem to have overshot the mark with the memory allocations; all processes are only using a fraction of what we're giving them. -We should dial that back down and save some resources. - -### 4.4. Adjust resource allocations for a specific process - -We can specify resource allocations for a given process using the `withName` process selector. -The syntax looks like this when it's by itself in a process block: +_After:_ -```groovy title="Syntax" +```groovy title="nextflow.config" linenums="4" process { - withName: 'GATK_JOINTGENOTYPING' { - cpus = 4 + memory = 1.GB + withName: 'cowpy' { + memory = 2.GB + cpus = 2 } } ``` -Let's add that to the existing process block in the `nextflow.config` file. +With this configuration, all processes will request 1GB of memory and a single CPU (the implied default), except the `cowpy` process, which will request 2GB and 2 CPUs. -```groovy title="nextflow.config" linenums="11" -process { - // defaults for all processes - cpus = 2 - memory = 2.GB - // allocations for a specific process - withName: 'GATK_JOINTGENOTYPING' { - cpus = 4 - } -} -``` +!!! note -With that specified, the default settings will apply to all processes **except** the `GATK_JOINTGENOTYPING` process, which is a special snowflake that gets a lot more CPU. -Hopefully that should have an effect. + If you have a machine with few CPUs and you allocate a high number per process, you might see process calls getting queued behind each other. + This is because Nextflow ensures we don't request more CPUs than are available. -### 4.5. Run again with the modified configuration +### 2.4. Run the workflow with the modified configuration -Let's run the workflow again with the modified configuration and with the reporting flag turned on, but notice we're giving the report a different name so we can differentiate them. +Let's try that out, supplying a different filename for the profiling report so we can compare performance before and after the configuration changes. ```bash -nextflow run main.nf -profile my_laptop -with-report report-config-2.html +nextflow run hello-config.nf -with-report report-config-2.html ``` -Once again, you probably won't notice a substantial difference in runtime, because this is such a small workload and the tools spend more time in ancillary tasks than in performing the 'real' work. - -However, the second report shows that our resource utilization is more balanced now. +You will probably not notice any real difference since this is such a small workload, but this is the approach you would use to analyze the performance and resource requirements of a real-world workflow. - - -As you can see, this approach is useful when your processes have different resource requirements. It empowers you to right-size the resource allocations you set up for each process based on actual data, not guesswork. +It is very useful when your processes have different resource requirements. It empowers you to right-size the resource allocations you set up for each process based on actual data, not guesswork. !!!note @@ -788,13 +279,14 @@ As you can see, this approach is useful when your processes have different resou We'll cover both of those approaches in an upcoming part of this training course. -That being said, there may be some constraints on what you can (or must) allocate depending on what computing executor and compute infrastructure you're using. For example, your cluster may require you to stay within certain limits that don't apply when you're running elsewhere. +### 2.5. Add resource limits -### 4.6. Add resource limits to an HPC profile +Depending on what computing executor and compute infrastructure you're using, there may be some constraints on what you can (or must) allocate. +For example, your cluster may require you to stay within certain limits. You can use the `resourceLimits` directive to set the relevant limitations. The syntax looks like this when it's by itself in a process block: -```groovy title="Syntax" +```groovy title="Syntax example" process { resourceLimits = [ memory: 750.GB, @@ -804,256 +296,179 @@ process { } ``` -Let's add this to the `univ_hpc` profile we set up earlier. - -_Before:_ - -```groovy title="nextflow.config" - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - } -``` +Nextflow will translate these values into the appropriate instructions depending on the executor that you specified. -_After:_ - -```groovy title="nextflow.config" - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - process.resourceLimits = [ - memory: 750.GB, - cpus: 200, - time: 30.d - ] - } -``` - -We can't test this since we don't have a live connection to Slurm in the Gitpod environment. -However, you can try running the workflow with resource allocations that exceed these limits, then look up the `sbatch` command in the `.command.run` script file. -You should see that the requests that actually get sent to the executor are capped at the values specified by `resourceLimits`. +We're not going to run this, since we don't have access to relevant infrastructure in the training environment. +However, if you were to try running the workflow with resource allocations that exceed these limits, then look up the `sbatch` command in the `.command.run` script file, you would see that the requests that actually get sent to the executor are capped at the values specified by `resourceLimits`. !!!note The nf-core project has compiled a [collection of configuration files](https://nf-co.re/configs/) shared by various institutions around the world, covering a wide range of HPC and cloud executors. - Those shared configs are valuable both for people who work there and can therefore just utilize their institution's configuration out of the box, and for people who are looking to develop a configuration for their own infrastructure. + Those shared configs are valuable both for people who work there and can therefore just utilize their institution's configuration out of the box, and as a model for people who are looking to develop a configuration for their own infrastructure. ### Takeaway -You know how to allocate process resources, tweak those allocations based on the utilization report, and use a profile to adapt the allocations to the compute environment. +You know how to generate a profiling report to assess resource utilization and how to modify resource allocations for all processes and/or for individual processes, as well as set resource limitations for running on HPC. ### What's next? -Configuring the parameters destined for the tools and operations wrapped within processes. +Learn to use a parameter file to store workflow parameters. --- -## 5. Configure workflow parameters - -So far we've been exploring options for configuring how Nextflow behaves in terms of executing the work. -That's all well and good, but how do we manage the parameters that are meant for the workflow itself, and the tools it calls within the processes? -That is also something we should be able to do without editing code files every time we want to run on some new data or switch to a different set of reference files. - -As it turns out, there's a lot of overlap between this kind of configuration and the infrastructure configuration, starting with the `nextflow.config` file, which can also house default values for command line parameters. - -### 5.1. Move the default parameter declarations to the configuration file - -We originally stored all our default parameter values in the workflow script itself, but we can move them out into the `nextflow.config` file if we prefer. +## 3. Use a parameter file to store workflow parameters -So let's cut this set of params out of `main.nf`: +So far we've been looking at configuration from the technical point of view of the compute infrastructure. +Now let's consider another aspect of workflow configuration that is very important for reproducibility: the configuration of the workflow parameters. -```groovy title="main.nf" linenums="3" -/* - * Pipeline parameters - */ +Currently, our workflow is set up to accept several parameter values via the command-line, with default values set in the workflow script itself. +This is fine for a simple workflow with very few parameters that need to be set for a given run. +However, many real-world workflows will have many more parameters that may be run-specific, and putting all of them in the command line would be tedious and error-prone. -// Primary input (file of input files, one per line) -params.reads_bam = "${projectDir}/data/sample_bams.txt" +Nextflow allows us to specify parameters via a parameter file in JSON format, which makes it very convenient to manage and distribute alternative sets of default values, for example, as well as run-specific parameter values. -// Output directory -params.outdir = 'results_genomics' +We provide an example parameter file in the current directory, called `test-params.json`: -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -// Base name for final output file -params.cohort_name = "family_trio" +```json title="test-params.json" linenums="1" +{ + "greeting": "greetings.csv", + "batch": "Trio", + "character": "turkey" +} ``` -And let's stick it into the `nextflow.config` file. +This parameter file contains a key-value pair for each of the inputs our workflow expects. -!!!note +### 3.1. Run the workflow using a parameter file - It doesn't really matter where we put it into the file, as long as we keep the params together and avoid mixing them in with the infrastructure configuration, for the sake of readability. - So putting it at the end will do just fine. - -### 5.2. Run the workflow with `-resume` to verify that it still works - -Let's check that we haven't broken anything, and let's include the `-resume` flag. +To run the workflow with this parameter file, simply add `-params-file ` to the base command. ```bash -nextflow run main.nf -profile my_laptop -resume +nextflow run hello-config.nf -params-file test-params.json ``` -Not only does everything work, but all of the process calls are recognized as having been run previously. +It works! And as expected, this produces the same outputs as previously. ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `main.nf` [modest_kay] DSL2 - revision: 328869237b +Launching `hello-config.nf` [disturbed_sammet] DSL2 - revision: ede9037d02 -[d6/353bb0] SAMTOOLS_INDEX (3) [100%] 3 of 3, cached: 3 ✔ -[dc/2a9e3f] GATK_HAPLOTYPECALLER (2) [100%] 3 of 3, cached: 3 ✔ -[fe/a940b2] GATK_JOINTGENOTYPING [100%] 1 of 1, cached: 1 ✔ +executor > local (8) +[f0/35723c] sayHello (2) | 3 of 3 ✔ +[40/3efd1a] convertToUpper (3) | 3 of 3 ✔ +[17/e97d32] collectGreetings | 1 of 1 ✔ +[98/c6b57b] cowpy | 1 of 1 ✔ +There were 3 greetings in this batch ``` -Indeed, having moved the parameter values to a different file changes nothing to the command submission that Nextflow generates. The resumability of the pipeline is preserved. +This may seem like overkill when you only have a few parameters to specify, but some pipelines expect dozens of parameters. +In those cases, using a parameter file will allow us to provide parameter values at runtime without having to type massive command lines and without modifying the workflow script. -### 5.3. Streamline the syntax of the parameter defaults - -Now that our default parameter declarations are in `nextflow.config`, we can switch to using a more structured syntax using a `params` block. That allows us to remove the repeated `params.`. - -```groovy title="nextflow.config" linenums="35" -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = "${projectDir}/data/sample_bams.txt" - - // Output directory - outdir = 'results_genomics' +### Takeaway - // Accessory files - reference = "${projectDir}/data/ref/ref.fasta" - reference_index = "${projectDir}/data/ref/ref.fasta.fai" - reference_dict = "${projectDir}/data/ref/ref.dict" - intervals = "${projectDir}/data/ref/intervals.bed" +You know how to manage parameter defaults and override them at runtime using a parameter file. - // Base name for final output file - cohort_name = "family_trio" -} -``` +### What's next? -Feel free to re-run this with the same command as above to verify that it works and still preserves the resumability of the pipeline. +Learn how to use profiles to conveniently switch between alternative configurations. -At this point, you may be wondering how to provide actual data and reference files to run this workflow for real, since what we've put in here is just a tiny test set. +--- -There are several options. -As we mentioned earlier (see note at the start of this page), you can override the defaults specified in the `nextflow.config` file by providing directives or parameter values on the command line, or by importing other configuration files. +## 3. Determine what executor(s) should be used to do the work -In this particular case, the best solution is to use a parameter file, which is a JSON file containing key-value pairs for all of the parameters you want to supply values for. +Until now, we have been running our pipeline with the local executor. +This executes each task on the machine that Nextflow is running on. +When Nextflow begins, it looks at the available CPUs and memory. +If the resources of the tasks ready to run exceed the available resources, Nextflow will hold the last tasks back from execution until one or more of the earlier tasks have finished, freeing up the necessary resources. -### 5.4. Using a parameter file to override defaults +For very large workloads, you may discover that your local machine is a bottleneck, either because you have a single task that requires more resources than you have available, or because you have so many tasks that waiting for a single machine to run them would take too long. +The local executor is convenient and efficient, but is limited to that single machine. +Nextflow supports [many different execution backends](https://www.nextflow.io/docs/latest/executor.html), including HPC schedulers (Slurm, LSF, SGE, PBS, Moab, OAR, Bridge, HTCondor and others) as well as cloud execution backends such (AWS Batch, Google Cloud Batch, Azure Batch, Kubernetes and more). -We provide a parameter file in the current directory, called `demo-params.json`, which contains key-value pairs for all of the parameters our workflow expects. -The values are the same input files and reference files we've been using so far. +Each of these systems uses different technologies, syntaxes and configurations for defining how a job should be defined. For example, /if we didn't have Nextflow/, a job requiring 8 CPUs and 4GB of RAM to be executed on the queue "my-science-work" would need to include the following configuration on SLURM and submit the job using `sbatch`: -```json title="demo-params.json" linenums="1" -{ - "reads_bam": "data/sample_bams.txt", - "outdir": "results_genomics", - "reference": "data/ref/ref.fasta", - "reference_index": "data/ref/ref.fasta.fai", - "reference_dict": "data/ref/ref.dict", - "intervals": "data/ref/intervals.bed", - "cohort_name": "family_trio" -} +```bash +#SBATCH -o /path/to/my/task/directory/my-task-1.log +#SBATCH --no-requeue +#SBATCH -c 8 +#SBATCH --mem 4096M +#SBATCH -p my-science-work ``` -To run the workflow with this parameter file, simply add `-params-file demo-params.json` to the base command. +If I wanted to make the workflow available to a colleague running on PBS, I'd need to remember to use a different submission program `qsub` and I'd need to change my scripts to use a new syntax for resources: ```bash -nextflow run main.nf -profile my_laptop -params-file demo-params.json +#PBS -o /path/to/my/task/directory/my-task-1.log +#PBS -j oe +#PBS -q my-science-work +#PBS -l nodes=1:ppn=5 +#PBS -l mem=4gb ``` -It works! And as expected, this produces the same outputs as previously. +If I wanted to use SGE, the configuration would be slightly different again: -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `main.nf` [marvelous_mandelbrot] DSL2 - revision: 328869237b - -executor > local (7) -[63/23a827] SAMTOOLS_INDEX (1) [100%] 3 of 3 ✔ -[aa/60aa4a] GATK_HAPLOTYPECALLER (2) [100%] 3 of 3 ✔ -[35/bda5eb] GATK_JOINTGENOTYPING [100%] 1 of 1 ✔ +```bash +#$ -o /path/to/my/task/directory/my-task-1.log +#$ -j y +#$ -terse +#$ -notify +#$ -q my-science-work +#$ -l slots=5 +#$ -l h_rss=4096M,mem_free=4096M ``` -However, you may be thinking, well, did we really override the configuration? How would we know, since those were the same files? +Running on a single cloud execution engine would require a new approach again, likely using an SDK that uses the cloud platform's APIs. -### 5.5. Remove or generalize default values from `nextflow.config` +Nextflow makes it easy to write a single workflow that can be run on each of these different infrastructures and systems, without having to modify the workflow. +The executor is subject to a process directive called `executor`. +By default it is set to `local`, so the following configuration is implied: -Let's strip out all the file paths from the `params` block in `nextflow.config`, replacing them with `null`, and replace the `cohort_name` value with something more generic. - -_Before:_ - -```groovy title="nextflow.config" linenums="39" -params { - // Primary input (file of input files, one per line) - reads_bam = "${projectDir}/data/sample_bams.txt" +```groovy title="Built-in configuration" +process { + executor = 'local' +} +``` - // Output directory - outdir = 'results_genomics' +### 3.1. Targeting a different backend - // Accessory files - reference = "${projectDir}/data/ref/ref.fasta" - reference_index = "${projectDir}/data/ref/ref.fasta.fai" - reference_dict = "${projectDir}/data/ref/ref.dict" - intervals = "${projectDir}/data/ref/intervals.bed" +By default, this training environment does not include a running HPC schedulder, but if you were running on a system with SLURM installed, for example, you can have Nextflow convert the `cpus`, `memory`, `queue` and other process directives into the correct syntax at runtime by adding following lines to the `nextflow.config` file: - // Base name for final output file - cohort_name = "family_trio" +```groovy title="nextflow.config" +process { + executor = 'slurm' } ``` -_After:_ +And... that's it! As noted before, this does assume that Slurm itself is already set up for you, but this is really all Nextflow itself needs to know. + +Basically we are telling Nextflow to generate a Slurm submission script and submit it using an `sbatch` command. -```groovy title="nextflow.config" linenums="39" -params { - // Primary input (file of input files, one per line) - reads_bam = null +### Takeaway - // Output directory - outdir = null +You now know how to change the executor to use different kinds of computing infrastructure. - // Accessory files - reference = null - reference_index = null - reference_dict = null - intervals = null +### What's next? - // Base name for final output file - cohort_name = "my_cohort" -} -``` +Learn how to control the resources allocated for executing processes. + +--- -Now, if you run the same command again, it will still work. -So yes, we're definitely able to pull those parameter values from the parameter file. +## 4. Use profiles to select preset configurations -This is great because, with the parameter file in hand, we'll now be able to provide parameter values at runtime without having to type massive command lines **and** without modifying the workflow nor the default configuration. +You may want to switch between alternative settings depending on what computing infrastructure you're using. For example, you might want to develop and run small-scale tests locally on your laptop, then run full-scale workloads on HPC or cloud. -That being said, it was nice to be able to demo the workflow without having to keep track of filenames and such. Let's see if we can use a profile to replicate that behavior. +Nextflow lets you set up profiles that describe different configurations, which you can then select at runtime using a command-line argument, rather than having to modify the configuration file itself. -### 5.6. Create a demo profile +### 4.1. Create profiles for switching between local development and execution on HPC -Yes we can! We just need to retrieve the default parameter declarations as they were written in the original workflow (with the `params.*` syntax) and copy them into a new profile that we'll call `demo`. +Let's set up two alternative profiles; one for running small scale loads on a regular computer, where we'll use Docker containers, and one for running on a university HPC with a Slurm scheduler, where we'll use Conda packages. -_Before:_ +Add the following to your `nextflow.config` file: ```groovy title="nextflow.config" linenums="3" profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } my_laptop { process.executor = 'local' docker.enabled = true @@ -1070,16 +485,62 @@ profiles { } ``` -_After:_ +You see that for the university HPC, we're also specifying resource limitations. -```groovy title="nextflow.config" linenums="3" -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true +### 4.2. Run the workflow with a profile + +To specify a profile in our Nextflow command line, we use the `-profile` argument. + +Let's try running the workflow with the `my_laptop` configuration. + +```bash +nextflow run hello-config.nf -profile my_laptop +``` + +This still produces the following output: + +``` + N E X T F L O W ~ version 24.10.0 + +Launching `hello-config.nf` [gigantic_brazil] DSL2 - revision: ede9037d02 + +executor > local (8) +[58/da9437] sayHello (3) | 3 of 3 ✔ +[35/9cbe77] convertToUpper (2) | 3 of 3 ✔ +[67/857d05] collectGreetings | 1 of 1 ✔ +[37/7b51b5] cowpy | 1 of 1 ✔ +There were 3 greetings in this batch +``` + +As you can see, this allows us to toggle between configurations very conveniently at runtime. + +!!! warning + + The `univ_hpc` profile will not run properly in the training environment since we do not have access to a Slurm scheduler. + +If in the future we find other elements of configuration that are always co-occurring with these, we can simply add them to the corresponding profile(s). +We can also create additional profiles if there are other elements of configuration that we want to group together. + +### 4.3. Create a test profile + +Profiles are not only for infrastructure configuration. +We can also use them to set default values for workflow parameters, to make it easier for others to try out the workflow without having to gather appropriate input values themselves. +This is intended as an alternative to using a parameter file. + +The syntax for expressing default values is the same as when writing them into the workflow file itself, except we wrap them in a block named `test`: + +```groovy title="Syntax example" + test { + params. + params. + ... } +``` + +If we add a test profile for our workflow, the `profiles` block becomes: + +```groovy title="nextflow.config" linenums="4" +profiles { my_laptop { process.executor = 'local' docker.enabled = true @@ -1093,55 +554,60 @@ profiles { time: 30.d ] } - demo { - // Primary input (file of input files, one per line) - params.reads_bam = "data/sample_bams.txt" - - // Output directory - params.outdir = 'results_genomics' - - // Accessory files - params.reference = "data/ref/ref.fasta" - params.reference_index = "data/ref/ref.fasta.fai" - params.reference_dict = "data/ref/ref.dict" - params.intervals = "data/ref/intervals.bed" - - // Base name for final output file - params.cohort_name = "family_trio" + test { + params.greeting = 'greetings.csv' + params.batch = 'test-batch' + params.character = 'turkey' } } ``` -As long as we distribute the data bundle with the workflow code, this will enable anyone to quickly try out the workflow without having to supply their own inputs or pointing to the parameter file. Besides, we can provide URLs to where files are stored and Nextflow will download them automatically. +Just like for technical configuration profiles, you can set up multiple different profiles specifying parameters under any arbitrary name you like. + +### 4.4. Run the workflow locally with the test profile -### 5.7. Run with the demo profile +Conveniently, profiles are not mutually exclusive, so we can specify multiple profiles in our command line using the following syntax `-profile ,` (for any number of profiles). -Let's try that out: +!!! note + + If you combine profiles that set values for the same elements of configuration and are described in the same configuration file, Nextflow will resolve the conflict by using whichever value it read in last (_i.e._ whatever comes later in the file). + If the conflicting settings are set in different configuration sources, the default [order of precedence](https://www.nextflow.io/docs/latest/config.html) applies. + +Let's try adding the test profile to our previous command: ```bash -nextflow run main.nf -profile my_laptop,demo +nextflow run hello-config.nf -profile my_laptop,test ``` -And it works perfectly! +This should produce the following: ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `main.nf` [cheesy_shaw] DSL2 - revision: 328869237b +Launching `hello-config.nf` [gigantic_brazil] DSL2 - revision: ede9037d02 -executor > local (7) -[4f/5ea14f] SAMTOOLS_INDEX (1) [100%] 3 of 3 ✔ -[fc/761e86] GATK_HAPLOTYPECALLER (3) [100%] 3 of 3 ✔ -[8a/2f498f] GATK_JOINTGENOTYPING [100%] 1 of 1 ✔ +executor > local (8) +[58/da9437] sayHello (3) | 3 of 3 ✔ +[35/9cbe77] convertToUpper (2) | 3 of 3 ✔ +[67/857d05] collectGreetings | 1 of 1 ✔ +[37/7b51b5] cowpy | 1 of 1 ✔ +There were 3 greetings in this batch ``` -Imagine what we can do with this tooling in place. -For example, we could also add profiles with popular sets of reference files to save people the trouble of providing their own. + + +This means that as long as we distribute any test data files with the workflow code, anyone can quickly try out the workflow without having to supply their own inputs via the command line or a parameter file. + +!!! note + + We can even point to URLs for larger files that are stored externally. + Nextflow will download them automatically as long as there is an open connection. ### Takeaway -You know how to manage parameter defaults, override them at runtime using a parameter file, and set up profiles. +You know how to use profiles to select a preset configuration at runtime with minimal hassle. More generally, you know how to configure your workflow executions to suit different compute platforms and enhance the reproducibility of your analyses. ### What's next? -Celebrate and relax. Then we'll move on to learning how to modularize the workflow code for optimal maintainability and reuse. +Celebrate and give yourself a big pat on the back! You have completed your very first Nextflow developer course. +Then check out the training portal homepage for more training content that may be of interest. diff --git a/docs/hello_nextflow/07_hello_modules.md b/docs/hello_nextflow/07_hello_modules.md deleted file mode 100644 index 5dfdd78ab..000000000 --- a/docs/hello_nextflow/07_hello_modules.md +++ /dev/null @@ -1,411 +0,0 @@ -# Part 6: Hello Modules - -This section covers how to organize your workflow code to make development and maintenance of your pipeline more efficient and sustainable. -Specifically, we are going to demonstrate how to use **modules**. - -In Nextflow, a **module** is a single process definition that is encapsulated by itself in a standalone code file. -To use a module in a workflow, you just add a single-line import statement to your workflow code file; then you can integrate the process into the workflow the same way you normally would. - -Putting processes into individual modules makes it possible to reuse process definitions in multiple workflows without producing multiple copies of the code. -This makes the code more shareable, flexible and maintainable. - -!!!note - - It is also possible to encapsulate a section of a workflow as a 'subworkflow' that can be imported into a larger pipeline, but that is outside the scope of this training. - ---- - -## 0. Warmup - -When we started developing our workflow, we put everything in one single code file. -In Part 5 (Hello Config), we started turning our one-file workflow into a proper pipeline project. -We moved to the standard Nextflow convention of naming the workflow file `main.nf`, fleshed out the configuration file, and added a parameter file. - -Now it's time to tackle **modularizing** our code, _i.e._ extracting the process definitions into modules. - -We're going to be working with a clean set of project files inside the project directory called `hello-modules` (for Modules). - -### 0.1. Explore the `hello-modules` directory - -Let's move into the project directory. - -```bash -cd hello-modules -``` - -!!! warning - - If you're continuing on directly from Part 5, you'll need to move up one directory first. - ``` - cd ../hello-modules - ``` - -The `hello-modules` directory has the same content and structure that you're expected to end up with in `hello-config` on completion of Part 5. - -```console title="Directory contents" -hello-modules/ -├── demo-params.json -├── main.nf -└── nextflow.config -``` - -For a detailed description of these files, see the warmup section in Part 5. - -### 0.2. Create a symbolic link to the data - -Just like last time, we need to set up a symlink to the data. -To do so, run this command from inside the `hello-modules` directory: - -```bash -ln -s ../data data -``` - -This creates a symbolic link called `data` pointing to the data directory one level up. - -### 0.3 Run the workflow using the appropriate profiles - -Now that everything is in place, we should be able to run the workflow using the profiles we set up in Part 5. - -```bash -nextflow run main.nf -profile my_laptop,demo -``` - -And so it does. - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `main.nf` [special_brenner] DSL2 - revision: 5a07b4894b - -executor > local (7) -[26/60774a] SAMTOOLS_INDEX (1) | 3 of 3 ✔ -[5a/eb40c4] GATK_HAPLOTYPECALLER (2) | 3 of 3 ✔ -[8f/94ac86] GATK_JOINTGENOTYPING | 1 of 1 ✔ -``` - -Like previously, there will now be a `work` directory and a `results_genomics` directory inside your project directory. - -### Takeaway - -You're ready to start modularizing your workflow. - -### What's next? - -Learn how to create your first module following conventions inspired by the nf-core project. - ---- - -## 1. Create a module for the `SAMTOOLS_INDEX` process - -From a technical standpoint, you can create a module simply by copying the process definition into its own file, and you can name that file anything you want. -However, the Nextflow community has adopted certain conventions for code organization, influenced in large part by the [nf-core](https://nf-co.re) project (which we'll cover later in this training series). - -The convention for Nextflow modules is that the process definition should be written to a standalone file named `main.nf`, stored in a directory structure with three to four levels: - -```console title="Directory structure" -modules -└── local - └── () - └── - └── main.nf -``` - -By convention, all modules are stored in a directory named `modules`. -Additionally, the convention distinguishes _local_ modules (which are part of your project) from _remote_ modules contained in remote repositories. - -The next levels down are named after the toolkit (if there is one) then the tool itself. -If the process defined in the module invokes more than one tool, as the GATK_JOINTGENOTYPING does in our example workflow, the name of the module can be the name of the method, or something to that effect. - -For example, the module we create for the `SAMTOOLS_INDEX` process will live under `modules/local/samtools/index/`. - -```console title="Directory structure" -modules -└── local - └── samtools - └── index - └── main.nf -``` - -!!!note - - We will cover remote modules later in this training, when we introduce the [nf-core library of modules](https://nf-co.re/modules/). - -So let's get started. - -### 2.1. Create a directory to house the local module code for the `SAMTOOLS_INDEX` process - -Run this command to create the appropriate directory structure: - -```bash -mkdir -p modules/local/samtools/index -``` - -The `-p` flag takes care of creating parent directories as needed. - -### 2.2. Create a file stub for the `SAMTOOLS_INDEX` process module - -Now let's create an empty `main.nf` file for the module. - -```bash -touch modules/local/samtools/index/main.nf -``` - -This gives us a place to put the process code. - -### 2.3. Move the `SAMTOOLS_INDEX` process code to the module file - -Copy the whole process definition over from the workflow's `main.nf` file to the module's `main.nf` file, making sure to copy over the `#!/usr/bin/env nextflow` shebang too. - -```groovy title="hello-modules/modules/local/samtools/index/main.nf" linenums="1" -#!/usr/bin/env nextflow - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - conda "bioconda::samtools=1.20" - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} -``` - -Once that is done, delete the process definition from the workflow's `main.nf` file, but make sure to leave the shebang in place. - -### 2.4. Add an import declaration before the workflow block - -The syntax for importing a local module is fairly straightforward: - -```groovy title="Import declaration syntax" -include { } from './modules/local/>//main.nf' -``` - -Let's insert that above the workflow block and fill it out appropriately. - -_Before:_ - -```groovy title="hello-modules/main.nf" linenums="73" -workflow { -``` - -_After:_ - -```groovy title="hello-modules/main.nf" linenums="73" -// Include modules -include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf' - -workflow { -``` - -### 2.5. Run the workflow to verify that it does the same thing as before - -We're running the workflow with essentially the same code and inputs as before, so let's add the `-resume` flag and see what happens. - -```bash -nextflow run main.nf -profile my_laptop,demo -resume -``` - -Sure enough, Nextflow recognizes that it's still all the same work to be done, even if the code is split up into multiple files. - -```console title="Output" - N E X T F L O W ~ version 24.10.0 - - ┃ Launching `main.nf` [agitated_cuvier] DSL2 - revision: 0ce0cd0c04 - -[c3/0d53a4] SAMTOOLS_INDEX (3) | 3 of 3, cached: 3 ✔ -[c6/8c6c30] GATK_HAPLOTYPECALLER (1) | 3 of 3, cached: 3 ✔ -[38/82b2e2] GATK_JOINTGENOTYPING | 1 of 1, cached: 1 ✔ -``` - -So modularizing the code in the course of development does not break resumability! - -### Takeaway - -You know how to extract a process into a local module. - -### What's next? - -Practice making more modules. - ---- - -## 3. Repeat procedure for the remaining processes - -Once you've done one, you can do a million modules... -But let's just do two more for now. - -### 3.1. Create directories to house the code for the two GATK modules - -Since GATK_HAPLOTYPECALLER and GATK_JOINTGENOTYPING both run GATK tools, we'll house them both under a shared `gatk` directory. - -```bash -mkdir -p modules/local/gatk/haplotypecaller -mkdir -p modules/local/gatk/jointgenotyping -``` - -You can imagine how it'll be useful to have that optional directory for grouping modules at the toolkit level. - -### 3.2. Create file stubs for the process modules - -Now let's make the file stubs to put the code into. - -```bash -touch modules/local/gatk/haplotypecaller/main.nf -touch modules/local/gatk/jointgenotyping/main.nf -``` - -### 3.3. Move the process code to the module files - -And finally, move the code for each process to the corresponding `main.nf` file, making sure to copy the shebang line too each time. - -### 3.3.1. GATK_HAPLOTYPECALLER module - -```groovy title="hello-modules/modules/local/gatk/haplotypecaller/main.nf" linenums="1" -#!/usr/bin/env nextflow - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} -``` - -### 3.3.2. GATK_JOINTGENOTYPING module - -```groovy title="hello-modules/modules/local/gatk/jointgenotyping/main.nf" linenums="1" -#!/usr/bin/env nextflow - -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" , emit: vcf - path "${cohort_name}.joint.vcf.idx" , emit: idx - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} -``` - -### 3.4. Add import declarations to the workflow `main.nf` file - -Now all that remains is to add the import statements: - -_Before:_ - -```groovy title="hello-modules/main.nf" linenums="3" -// Include modules -include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf' - -workflow { -``` - -_After:_ - -```groovy title="hello-modules/main.nf" linenums="3" -// Include modules -include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf' -include { GATK_HAPLOTYPECALLER } from './modules/local/gatk/haplotypecaller/main.nf' -include { GATK_JOINTGENOTYPING } from './modules/local/gatk/jointgenotyping/main.nf' - -workflow { -``` - -### 3.5. Run the workflow to verify that everything still works as expected - -Look at that short `main.nf` file! Let's run it once last time. - -```bash -nextflow run main.nf -profile my_laptop,demo -resume -``` - -Yep, everything still works, including the resumability of the pipeline. - -```console title="Output" -N E X T F L O W ~ version 24.02.0-edge - -┃ Launching `main.nf` [tiny_blackwell] DSL2 - revision: 0ce0cd0c04 - -[62/21cdc5] SAMTOOLS_INDEX (1) | 3 of 3, cached: 3 ✔ -[c6/8c6c30] GATK_HAPLOTYPECALLER (2) | 3 of 3, cached: 3 ✔ -[38/82b2e2] GATK_JOINTGENOTYPING | 1 of 1, cached: 1 ✔ -``` - -Congratulations, you've done all this work and absolutely nothing has changed to how the pipeline works! - -Jokes aside, now your code is more modular, and if you decide to write another pipeline that calls on one of those processes, you just need to type one short import statement to use the relevant module. -This is better than just copy-pasting the code, because if later you decide to improve the module, all your pipelines will inherit the improvements. - -### Takeaway - -You know how to modularize multiple processes in a workflow. - -### What's next? - -Learn to add tests to your pipeline using the nf-test framework. diff --git a/docs/hello_nextflow/index.md b/docs/hello_nextflow/index.md index cfcb9c8bc..2be88cd58 100644 --- a/docs/hello_nextflow/index.md +++ b/docs/hello_nextflow/index.md @@ -12,7 +12,7 @@ The rise of big data has made it increasingly necessary to be able to analyze an During this training, you will be introduced to Nextflow in a series of complementary hands-on workshops. -Let's get started! +Let's get started! Click on the "Open in Gitpod" button below. [![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training) @@ -34,5 +34,5 @@ This is a workshop for those who are completely new to Nextflow. Some basic fami **Prerequisites** -- A GitHub account -- Experience with command line +- A GitHub account and Gitpod login OR a local installation as described [here](envsetup/02_local). +- Experience with command line and basic scripting diff --git a/docs/index.md b/docs/index.md index d1a01d491..9b8f25914 100644 --- a/docs/index.md +++ b/docs/index.md @@ -13,7 +13,7 @@ Welcome to the Nextflow community training portal! We have several distinct training courses available on this website. Scroll down to find the one that's right for you! -The training courses listed below are designed to be useable as a self-service resource; you can work through them on your own at any time (see Environment Setup for practical details). However, you may get even more out of them by joining a group training event. +The training courses listed below are designed to be usable as a self-service resource; you can work through them on your own at any time (see Environment Setup for practical details). However, you may get even more out of them by joining a group training event. - Free online events are run regularly by the nf-core community, see the [nf-core events page](https://nf-co.re/events) for more. - Seqera (the company that develops Nextflow) runs a variety of training events, see the [Seqera Events](https://seqera.io/events/) page and look for 'Seqera Sessions' and 'Nextflow Summit'. @@ -29,87 +29,117 @@ When you're ready to get down to work, click on the 'Open in Gitpod' button, eit !!! quote inline end "" - :material-lightbulb: Essential for setting up your environment for the first time. + :material-lightbulb: Set up your environment for the first time. - Instructions for setting up your environment to work through training materials (all courses). Provides an orientation to Gitpod as well as alternate installation instructions for working on your own local machine. + Instructions for setting up your environment to work through training materials (all courses). Provides an orientation to the training platform as well as alternate installation instructions for working on your own local machine. [Launch the Environment Setup training :material-arrow-right:](envsetup/index.md){ .md-button .md-button--primary } ## Nextflow for Newcomers +These are foundational, domain-agnostic courses intended for those who are completely new to Nextflow. Each course consists of a series of training modules that are designed to help learners build up their skills progressively. + !!! exercise "Hello Nextflow" !!! quote inline end "" - :material-run-fast: A modular training series for getting started with Nextflow. + :material-run-fast: Learn to develop pipelines in Nextflow. - This is a foundational course for those who are completely new to Nextflow. It consists of a series of training modules that are designed to help learners build up their skills progressively. The series covers the core components of the Nextflow language as well as essential pipeline design and development practices, and effective use of third-party resources. + This is a course for newcomers who wish to learn how to develop their own pipelines. The course covers the core components of the Nextflow language in enough detail to enable developing simple but fully functional pipelines. It also covers key elements of pipeline design, development and configuration practices. - [Launch the Hello Nextflow training :material-arrow-right:](hello_nextflow/index.md){ .md-button } + [Launch the Hello Nextflow training :material-arrow-right:](hello_nextflow/index.md){ .md-button .md-button--primary } -## In-depth Nextflow Training +**Coming soon:** "Nextflow Run" — Learn to run Nextflow pipelines (run only, no code development) -!!! exercise "Fundamentals Training" + -!!! exercise "Advanced Training" +## Nextflow for Science + +These are courses that demonstrate how to apply the concepts and components presented in 'Hello Nextflow' (see above) to specific scientific use cases. Each course consists of a series of training modules that are designed to help learners build up their skills progressively. + +!!! exercise "Nextflow for Genomics" !!! quote inline end "" - :material-lightbulb: Advanced training material for mastering Nextflow. + :material-run-fast: Learn to develop a pipeline for genomics in Nextflow. - Advanced material exploring the more advanced features of the Nextflow language and runtime, and how to use them to write efficient and scalable data-intensive workflows. + This is a course for researchers who wish to learn how to develop their own genomics pipelines. The course uses a variant calling use case to demonstrate how to develop a simple but functional genomics pipeline. - [Launch the Advanced Training :material-arrow-right:](advanced/index.md){ .md-button .md-button--primary } + [Launch the Nextflow for Genomics training :material-arrow-right:](nf4_science/genomics/){ .md-button .md-button--primary } -## Other/Experimental +**Coming soon:** "Nextflow for RNAseq" — Learn to develop a pipeline for bulk RNAseq analysis in Nextflow -!!! exercise "Configure the execution of an nf-core pipeline" + + +## In-depth Nextflow Training - [Launch the nf-core configuration training :material-arrow-right:](nf_customize/index.md){ .md-button } +These are courses that demonstrate how to use Nextflow features in more detail or at a more advanced level. Each course consists of one or more training modules that are designed to help learners hone their skills on the corresponding topics. -!!! exercise "Develop a pipeline with the nf-core template" + -!!! exercise "Troubleshooting exercises" +!!! exercise "Fundamentals Training" + + !!! tip inline end "" + + :material-lightbulb: Comprehensive training material for exploring the full scope of Nextflow's capabilities. + + The fundamentals training material covers all things Nextflow. Intended as a reference material for anyone looking to build complex workflows with Nextflow. + + [Launch the Fundamentals Training :material-arrow-right:](basic_training/index.md){ .md-button .md-button--primary } + +!!! exercise "Advanced Training" !!! quote inline end "" - :material-run-fast: This course will help you troubleshooting common pipeline errors. + :material-lightbulb: Advanced training material for mastering Nextflow. + + Advanced material exploring the more advanced features of the Nextflow language and runtime, and how to use them to write efficient and scalable data-intensive workflows. - A "learn by doing" troubleshooting tutorial for pipeline developers and users. + [Launch the Advanced Training :material-arrow-right:](advanced/index.md){ .md-button .md-button--primary } - [Launch the Troubleshooting training :material-arrow-right:](troubleshoot/index.md){ .md-button } +## Other/Experimental -## Deprecated +These are training courses that are not being actively taught/maintained and that we may repurpose elsewhere or delete in the near future. +The corresponding materials are not available within the training environment. +You can still find the materials in the GitHub repository and download them for local use. -!!! exercise "Simple RNA-seq variant calling" +- **nf-customize** — Configuring nf-core pipelines ([docs](other/nf_customize) / [code](../other/nf-customize)) - !!! quote inline end "" +- **nf-develop** — Developing a pipeline with the nf-core template ([docs](other/nf_develop) / [code](../other/nf-develop)) - :material-run-fast: A short hands-on tutorial focused on a concrete analysis pipeline example. +- **troubleshoot** — Troubleshooting exercises ([docs](other/troubleshoot) / [code](../other/troubleshoot)) - This course was developed as a "learn by doing" tutorial intended as a fast, hands-on way to get to grips with Nextflow using a very concrete analysis pipeline example. You can still find the materials in the GitHub repository, but it is no longer being maintained and can no longer be launched in Gitpod or in the training portal. +- **hands-on (rnaseq)** — Developing a pipeline for bulk RNAseq (deprecated) ([docs](other/hands_on) / [code](../other/hands-on)) ## Resources diff --git a/docs/nextflow_run/01_orientation.md b/docs/nextflow_run/01_orientation.md new file mode 100644 index 000000000..4353bdd7f --- /dev/null +++ b/docs/nextflow_run/01_orientation.md @@ -0,0 +1,46 @@ +# Orientation + +The Gitpod environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. +However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface. + +If you have not yet done so, please follow [this link](../../envsetup/) before going any further. + +## Materials provided + +Throughout this training course, we'll be working in the `run-nextflow/` directory. +This directory contains all the code files, test data and accessory files you will need. + +Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the Gitpod workspace. +Alternatively, you can use the `tree` command. +Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity. + +Here we generate a table of contents to the second level down: + +```bash +tree . -L 2 +``` + +If you run this inside `run-nextflow`, you should see the following output: [TODO] + +```console title="Directory contents" +. +``` + +!!!note + + Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course. + This is just meant to give you an overview. + +**Here's a summary of what you should know to get started:** + +[TODO] + +!!!tip + + If for whatever reason you move out of this directory, you can always run this command to return to it: + + ```bash + cd /workspace/gitpod/run-nextflow + ``` + +Now, to begin the course, click on the arrow in the bottom right corner of this page. diff --git a/docs/nextflow_run/02_run_basics.md b/docs/nextflow_run/02_run_basics.md new file mode 100644 index 000000000..14f0b7e56 --- /dev/null +++ b/docs/nextflow_run/02_run_basics.md @@ -0,0 +1,10 @@ +# Part 1: Run Basics + +[TODO] + +Should cover: + +- basic project structure (main.nf, modules, nextflow.config) +- run from CLI (re-use from Hello-World) +- basic config elements (refer to hello-config) including profiles +- running resource profiling and adapting the config diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/nextflow_run/03_run_nf-core.md similarity index 99% rename from docs/hello_nextflow/09_hello_nf-core.md rename to docs/nextflow_run/03_run_nf-core.md index c0e3ade52..b017884df 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/nextflow_run/03_run_nf-core.md @@ -1,4 +1,4 @@ -# Part 8: Hello nf-core +# Part 3: Run nf-core nf-core is a community effort to develop and maintain a curated set of analysis pipelines built using Nextflow. @@ -1194,7 +1194,7 @@ This section should feel familiar to the `hello_modules` section. If you have a module that you would like to contribute back to the community, reach out on the nf-core slack or open a pull request to the modules repository. -Start by using the nf-core tooling to create a sceleton local module: +Start by using the nf-core tooling to create a skeleton local module: ```console nf-core modules create diff --git a/docs/hello_nextflow/10_hello_seqera.md b/docs/nextflow_run/04_run_seqera.md similarity index 100% rename from docs/hello_nextflow/10_hello_seqera.md rename to docs/nextflow_run/04_run_seqera.md diff --git a/docs/nextflow_run/img/cpu-after.png b/docs/nextflow_run/img/cpu-after.png new file mode 100644 index 000000000..f173ef020 Binary files /dev/null and b/docs/nextflow_run/img/cpu-after.png differ diff --git a/docs/nextflow_run/img/cpu-before.png b/docs/nextflow_run/img/cpu-before.png new file mode 100644 index 000000000..e0b8c76c8 Binary files /dev/null and b/docs/nextflow_run/img/cpu-before.png differ diff --git a/docs/nextflow_run/img/memory-after.png b/docs/nextflow_run/img/memory-after.png new file mode 100644 index 000000000..d61b4a7c5 Binary files /dev/null and b/docs/nextflow_run/img/memory-after.png differ diff --git a/docs/nextflow_run/img/memory-before.png b/docs/nextflow_run/img/memory-before.png new file mode 100644 index 000000000..ce0f7ac27 Binary files /dev/null and b/docs/nextflow_run/img/memory-before.png differ diff --git a/docs/hello_nextflow/img/nested.excalidraw.svg b/docs/nextflow_run/img/nested.excalidraw.svg similarity index 100% rename from docs/hello_nextflow/img/nested.excalidraw.svg rename to docs/nextflow_run/img/nested.excalidraw.svg diff --git a/docs/hello_nextflow/img/nf-core-modules.png b/docs/nextflow_run/img/nf-core-modules.png similarity index 100% rename from docs/hello_nextflow/img/nf-core-modules.png rename to docs/nextflow_run/img/nf-core-modules.png diff --git a/docs/hello_nextflow/img/pipeline.excalidraw.svg b/docs/nextflow_run/img/pipeline.excalidraw.svg similarity index 100% rename from docs/hello_nextflow/img/pipeline.excalidraw.svg rename to docs/nextflow_run/img/pipeline.excalidraw.svg diff --git a/docs/hello_nextflow/img/pipeline_schema.png b/docs/nextflow_run/img/pipeline_schema.png similarity index 100% rename from docs/hello_nextflow/img/pipeline_schema.png rename to docs/nextflow_run/img/pipeline_schema.png diff --git a/docs/nextflow_run/img/report_cover.png b/docs/nextflow_run/img/report_cover.png new file mode 100644 index 000000000..9feb1792c Binary files /dev/null and b/docs/nextflow_run/img/report_cover.png differ diff --git a/docs/hello_nextflow/img/seqera-containers-1.png b/docs/nextflow_run/img/seqera-containers-1.png similarity index 100% rename from docs/hello_nextflow/img/seqera-containers-1.png rename to docs/nextflow_run/img/seqera-containers-1.png diff --git a/docs/hello_nextflow/img/seqera-containers-2.png b/docs/nextflow_run/img/seqera-containers-2.png similarity index 100% rename from docs/hello_nextflow/img/seqera-containers-2.png rename to docs/nextflow_run/img/seqera-containers-2.png diff --git a/docs/nextflow_run/index.md b/docs/nextflow_run/index.md new file mode 100644 index 000000000..66eaedaa1 --- /dev/null +++ b/docs/nextflow_run/index.md @@ -0,0 +1,39 @@ +--- +title: Run Nextflow +hide: + - toc +--- + +# Run Nextflow + +Hello! You are now on the path to running reproducible and scalable scientific workflows using Nextflow. + +[TODO] NEED TO DISTINGUISH CLEARLY FROM HELLO NEXTFLOW + +The rise of big data has made it increasingly necessary to be able to analyze and perform experiments on large datasets in a portable and reproducible manner. Parallelization and distributed computing are the best ways to tackle this challenge, but the tools commonly available to computational scientists often lack good support for these techniques, or they provide a model that fits poorly with the needs of computational scientists. Nextflow was particularly created to address these challenges. + +During this training, you will be introduced to Nextflow in a series of complementary hands-on workshops. + +Let's get started! + +[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training) + +## Learning objectives + +In this workshop, you will learn foundational concepts for building pipelines. + +By the end of this workshop you will be able to: + +- Launch a Nextflow workflow locally +- Find and interpret outputs (results) and log files generated by Nextflow +- Troubleshoot basic issues +- [TODO] + +## Audience & prerequisites + +This is a workshop for those who are completely new to Nextflow. Some basic familiarity with the command line, and common file formats is assumed. + +**Prerequisites** + +- A GitHub account +- Experience with command line diff --git a/docs/hello_nextflow/seqera/01_run_with_cli.md b/docs/nextflow_run/seqera/01_run_with_cli.md similarity index 100% rename from docs/hello_nextflow/seqera/01_run_with_cli.md rename to docs/nextflow_run/seqera/01_run_with_cli.md diff --git a/docs/hello_nextflow/seqera/02_run_with_launchpad.md b/docs/nextflow_run/seqera/02_run_with_launchpad.md similarity index 100% rename from docs/hello_nextflow/seqera/02_run_with_launchpad.md rename to docs/nextflow_run/seqera/02_run_with_launchpad.md diff --git a/docs/hello_nextflow/seqera/img/compute_env_platforms.png b/docs/nextflow_run/seqera/img/compute_env_platforms.png similarity index 100% rename from docs/hello_nextflow/seqera/img/compute_env_platforms.png rename to docs/nextflow_run/seqera/img/compute_env_platforms.png diff --git a/docs/hello_nextflow/seqera/img/launchpad.gif 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docs/nextflow_run/seqera/img/usage_token.png diff --git a/docs/nf4_science/genomics/00_orientation.md b/docs/nf4_science/genomics/00_orientation.md new file mode 100644 index 000000000..990854331 --- /dev/null +++ b/docs/nf4_science/genomics/00_orientation.md @@ -0,0 +1,68 @@ +# Orientation + +The training environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. +However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface. + +If you have not yet done so, please follow [this link](../../envsetup/) before going any further. + +## Materials provided + +Throughout this training course, we'll be working in the `nf4-science/genomics/` directory, which you need to move into when you open the training workspace. +This directory contains all the code files, test data and accessory files you will need. + +Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the training workspace in the VSCode interface. +Alternatively, you can use the `tree` command. +Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity. + +Here we generate a table of contents to the second level down: + +```bash +tree . -L 2 +``` + +If you run this inside `nf4-science/genomics`, you should see the following output: + +```console title="Directory contents" + +. +├── data +│ ├── bam +│ ├── ref +│ ├── sample_bams.txt +│ └── samplesheet.csv +├── genomics-1.nf +├── genomics-2.nf +└── solutions + +4 directories, 2 files + +``` + +!!!note + + Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course. + This is just meant to give you an overview. + +**Here's a summary of what you should know to get started:** + +- **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in. + +- **The file `nextflow.config`** is a configuration file that sets minimal environment properties. + You can ignore it for now. + +- \*\*The `data` directory contains input data and related resources, described later in the course. + +- **The `solutions` directory** contains the completed workflow scripts that result from each step of the course. + They are intended to be used as a reference to check your work and troubleshoot any issues. + The name and number in the filename correspond to the step of the relevant part of the course. + For example, the file `TODO.nf` is the expected result of completing steps X through Y of Part 1: TODO. + +!!!tip + + If for whatever reason you move out of this directory, you can always run this command to return to it: + + ```bash + cd /workspace/gitpod/nf4-science/genomics + ``` + +Now, to begin the course, click on the arrow in the bottom right corner of this page. diff --git a/docs/hello_nextflow/04_hello_genomics.md b/docs/nf4_science/genomics/01_per_sample_variant_calling.md similarity index 80% rename from docs/hello_nextflow/04_hello_genomics.md rename to docs/nf4_science/genomics/01_per_sample_variant_calling.md index b1b3e5227..1a26b96a4 100644 --- a/docs/hello_nextflow/04_hello_genomics.md +++ b/docs/nf4_science/genomics/01_per_sample_variant_calling.md @@ -1,15 +1,6 @@ -# Part 3: Hello Genomics +# Part 1: Per-sample variant calling -In Part 1, you learned how to use the basic building blocks of Nextflow to assemble a simple pipeline capable of processing some text and parallelizing execution if there were multiple inputs. -Then in Part 2, you learned how to use containers to pull in command line tools to test them and integrate them into your pipelines without having to deal with software dependency issues. - -Now, we show you how to use the same components and principles to build a pipeline that does something a bit more interesting, and hopefully a bit more relatable to your work. -Specifically, we show you how to implement a simple variant calling pipeline with [GATK](https://gatk.broadinstitute.org/) (Genome Analysis Toolkit), a widely used software package for analyzing high-throughput sequencing data. - -!!! note - - Don't worry if you're not familiar with GATK or genomics in general. - We'll summarize the necessary concepts as we go, and the workflow implementation principles we demonstrate here apply broadly to any command line tool that takes in some input files and produce some output files. +In the first part of this course, we show you how to build a simple variant calling pipeline that applies GATK variant calling to individual sequencing samples. ### Method overview @@ -18,43 +9,44 @@ Here we are going to use tools and methods designed for calling short variants, ![GATK pipeline](img/gatk-pipeline.png) -A full variant calling pipeline typically involves a lot of steps, including mapping to the reference and variant filtering and prioritization. -For simplicity, we are going to focus on the core variant calling step, which takes as its main input a file of short-read sequencing data in [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) format (Binary Alignment Map, a compressed version of SAM, Sequence Alignment Map), as well as a reference genome and a list of genomic intervals to analyze. +A full variant calling pipeline typically involves a lot of steps, including mapping to the reference (sometime referred to as genome alignment) and variant filtering and prioritization. +For simplicity, in this part of the course we are going to focus on just the variant calling part. -For this exercise, we provide you with three samples in BAM format (see Dataset below). -However, GATK requires an index file for each BAM file, which we did not provide (on purpose), so the workflow will have to create one as a preliminary step. +### Dataset -!!! note +We provide the following data and related resources: - Index files are a common feature of bioinformatics file formats; they contain information about the structure of the main file that allows tools like GATK to access a subset of the data without having to read through the whole file. - This is important because of how big these files can get. +- **A reference genome** consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and sequence dictionary). +- **Three whole genome sequencing samples** corresponding to a family trio (mother, father and son), which have been subset to a small slice of data on chromosome 20 to keep the file sizes small. + This is Illumina short-read sequencing data that have already been mapped to the reference genome, provided in [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) format (Binary Alignment Map, a compressed version of SAM, Sequence Alignment Map). +- **A list of genomic intervals**, i.e. coordinates on the genome where our samples have data suitable for calling variants, provided in BED format. + +### Workflow -So to recap, we're going to develop a workflow that does the following: +In this part of the course, we're going to develop a workflow that does the following: 1. Generate an index file for each BAM input file using [Samtools](https://www.htslib.org/) 2. Run the GATK HaplotypeCaller on each BAM input file to generate per-sample variant calls in VCF (Variant Call Format)
---8<-- "docs/hello_nextflow/img/hello-gatk-1.svg" +--8<-- "docs/nf4_science/genomics/img/hello-gatk-1.svg"
-### Dataset +!!! note -- **A reference genome** consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and sequence dictionary). -- **Three whole genome sequencing samples** corresponding to a family trio (mother, father and son), which have been subset to a small slice of data on chromosome 20 to keep the file sizes small. - The sequencing data is in (Binary Alignment Map) format, i.e. genome sequencing reads that have already been mapped to the reference genome. -- **A list of genomic intervals**, i.e. coordinates on the genome where our samples have data suitable for calling variants, provided in BED format. + Index files are a common feature of bioinformatics file formats; they contain information about the structure of the main file that allows tools like GATK to access a subset of the data without having to read through the whole file. + This is important because of how big these files can get. --- ## 0. Warmup: Test the Samtools and GATK commands interactively -Just like in the Hello World example, we want to try out the commands manually before we attempt to wrap them in a workflow. -The tools we need (Samtools and GATK) are not installed in the Gitpod environment, but that's not a problem since you learned how to work with containers in Part 2 of this training series (Hello Containers). +First we want to try out the commands manually before we attempt to wrap them in a workflow. +The tools we need (Samtools and GATK) are not installed in the Gitpod environment, so we'll use them via containers (see [Hello Containers](../../hello_nextflow/05_hello_containers.md)). !!! note - Make sure you're in the `hello-nextflow` directory so that the last part of the path shown when you type `pwd` is `hello-nextflow`. + Make sure you're in the `nf4-science/genomics` directory so that the last part of the path shown when you type `pwd` is `genomics`. ### 0.1. Index a BAM input file with Samtools @@ -165,14 +157,14 @@ Learn how to wrap those same commands into a two-step workflow that uses contain ## 1. Write a single-stage workflow that runs Samtools index on a BAM file -We provide you with a workflow file, `hello-genomics.nf`, that outlines the main parts of the workflow. +We provide you with a workflow file, `genomics-1.nf`, that outlines the main parts of the workflow. It's not functional; its purpose is just to serve as a skeleton that you'll use to write the actual workflow. ### 1.1. Define the indexing process Let's start by writing a process, which we'll call `SAMTOOLS_INDEX`, describing the indexing operation. -```groovy title="hello-genomics.nf" linenums="9" +```groovy title="genomics-1.nf" linenums="9" /* * Generate BAM index file */ @@ -208,7 +200,7 @@ This process is going to require us to pass in a file path via the `input_bam` i At the top of the file, under the `Pipeline parameters` section, we declare a CLI parameter called `reads_bam` and give it a default value. That way, we can be lazy and not specify the input when we type the command to launch the pipeline (for development purposes). We're also going to set `params.outdir` with a default value for the output directory. -```groovy title="hello-genomics.nf" linenums="3" +```groovy title="genomics-1.nf" linenums="3" /* * Pipeline parameters */ @@ -220,9 +212,11 @@ params.outdir = "results_genomics" Now we have a process ready, as well as a parameter to give it an input to run on, so let's wire those things up together. + + !!! note - `${projectDir}` is a built-in Nextflow variable that points to the directory where the current Nextflow workflow script (`hello-genomics.nf`) is located. + `${projectDir}` is a built-in Nextflow variable that points to the directory where the current Nextflow workflow script (`genomics-1.nf`) is located. This makes it easy to reference files, data directories, and other resources included in the workflow repository without hardcoding absolute paths. @@ -230,7 +224,7 @@ Now we have a process ready, as well as a parameter to give it an input to run o In the `workflow` block, we need to set up a **channel** to feed the input to the `SAMTOOLS_INDEX` process; then we can call the process itself to run on the contents of that channel. -```groovy title="hello-genomics.nf" linenums="30" +```groovy title="genomics-1.nf" linenums="30" workflow { // Create input channel (single file via CLI parameter) @@ -241,16 +235,16 @@ workflow { } ``` -You'll notice we're using the same `.fromPath` channel factory as we used at the end of Part 1 (Hello World) of this training series. +You'll notice we're using the same `.fromPath` channel factory as we used in [Hello Channels](../../hello_nextflow/02_hello_channels.md). Indeed, we're doing something very similar. -The difference is that this time we're telling Nextflow to load the file path itself into the channel as an input element, rather than reading in its contents. +The difference is that we're telling Nextflow to just load the file path itself into the channel as an input element, rather than reading in its contents. ### 1.4. Run the workflow to verify that the indexing step works Let's run the workflow! As a reminder, we don't need to specify an input in the command line because we set up a default value for the input when we declared the input parameter. ```bash -nextflow run hello-genomics.nf +nextflow run genomics-1.nf ``` The command should produce something like this: @@ -258,7 +252,7 @@ The command should produce something like this: ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `hello-genomics.nf` [reverent_sinoussi] DSL2 - revision: 41d43ad7fe + ┃ Launching `genomics-1.nf` [reverent_sinoussi] DSL2 - revision: 41d43ad7fe executor > local (1) [2a/e69536] SAMTOOLS_INDEX (1) | 1 of 1 ✔ @@ -268,7 +262,7 @@ You can check that the index file has been generated correctly by looking in the ```console title="Directory contents" work/2a/e695367b2f60df09cf826b07192dc3 -├── reads_mother.bam -> /workspace/gitpod/hello-nextflow/data/bam/reads_mother.bam +├── reads_mother.bam -> /workspace/gitpod/nf4-science/genomics/data/bam/reads_mother.bam └── reads_mother.bam.bai ``` @@ -281,7 +275,7 @@ There it is! ### Takeaway -You know how to wrap a real bioinformatics tool in a single-step Nextflow workflow and have it run using a container. +You know how to wrap a genomics tool in a single-step Nextflow workflow and have it run using a container. ### What's next? @@ -297,7 +291,7 @@ Now that we have an index for our input file, we can move on to setting up the v Let's write a process, which we'll call `GATK_HAPLOTYPECALLER`, describing the variant calling operation. -```groovy title="hello-genomics.nf" linenums="30" +```groovy title="genomics-1.nf" linenums="30" /* * Call variants with GATK HaplotypeCaller */ @@ -348,7 +342,7 @@ Similarly, we have to list the output VCF's index file (the `"${input_bam}.vcf.i Since our new process expects a handful of additional files to be provided, we set up some CLI parameters for them under the `Pipeline parameters` section, along with some default values (same reasons as before). -```groovy title="hello-genomics.nf" linenums="10" +```groovy title="genomics-1.nf" linenums="10" // Accessory files params.reference = "${projectDir}/data/ref/ref.fasta" params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" @@ -362,7 +356,7 @@ While main data inputs are streamed dynamically through channels, there are two Add this to the workflow block (after the `reads_ch` creation): -```groovy title="hello-genomics.nf" linenums="71" +```groovy title="genomics-1.nf" linenums="71" // Load the file paths for the accessory files (reference and intervals) ref_file = file(params.reference) ref_index_file = file(params.reference_index) @@ -376,7 +370,7 @@ This will make the accessory file paths available for providing as input to any Now that we've got our second process set up and all the inputs and accessory files are ready and available, we can add a call to the `GATK_HAPLOTYPECALLER` process in the workflow body. -```groovy title="hello-genomics.nf" linenums="80" +```groovy title="genomics-1.nf" linenums="80" // Call variants from the indexed BAM file GATK_HAPLOTYPECALLER( reads_ch, @@ -400,7 +394,7 @@ You should recognize the `*.out` syntax from Part 1 of this training series; we Let's run the expanded workflow with `-resume` so that we don't have to run the indexing step again. ```bash -nextflow run hello-genomics.nf -resume +nextflow run genomics-1.nf -resume ``` Now if we look at the console output, we see the two processes listed: @@ -408,7 +402,7 @@ Now if we look at the console output, we see the two processes listed: ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `hello-genomics.nf` [grave_volta] DSL2 - revision: 4790abc96a + ┃ Launching `genomics-1.nf` [grave_volta] DSL2 - revision: 4790abc96a executor > local (1) [2a/e69536] SAMTOOLS_INDEX (1) | 1 of 1, cached: 1 ✔ @@ -422,8 +416,8 @@ You'll find the output file `reads_mother.bam.vcf` in the results directory, as ```console title="Directory contents" results_genomics/ ├── reads_mother.bam.bai -├── reads_mother.bam.vcf -> /workspace/gitpod/hello-nextflow/work/53/e18e987d56c47f59b7dd268649ec01/reads_mother.bam.vcf -└── reads_mother.bam.vcf.idx -> /workspace/gitpod/hello-nextflow/work/53/e18e987d56c47f59b7dd268649ec01/reads_mother.bam.vcf.idx +├── reads_mother.bam.vcf -> /workspace/gitpod/nf4-science/genomics/work/53/e18e987d56c47f59b7dd268649ec01/reads_mother.bam.vcf +└── reads_mother.bam.vcf.idx -> /workspace/gitpod/nf4-science/genomics/work/53/e18e987d56c47f59b7dd268649ec01/reads_mother.bam.vcf.idx ``` If you open the VCF file, you should see the same contents as in the file you generated by running the GATK command directly in the container. @@ -439,7 +433,7 @@ This is the output we care about generating for each sample in our study. ### Takeaway -You know how to make a very basic two-step workflow that does real analysis work and is capable of dealing with bioinformatics idiosyncrasies like the accessory files. +You know how to make a very basic two-step workflow that does real analysis work and is capable of dealing with genomics file format idiosyncrasies like the accessory files. ### What's next? @@ -460,14 +454,14 @@ Let's turn that default file path in the input BAM file declaration into an arra _Before:_ -```groovy title="hello-genomics.nf" linenums="7" +```groovy title="genomics-1.nf" linenums="7" // Primary input params.reads_bam = "${projectDir}/data/bam/reads_mother.bam" ``` _After:_ -```groovy title="hello-genomics.nf" linenums="7" +```groovy title="genomics-1.nf" linenums="7" // Primary input (array of three samples) params.reads_bam = [ "${projectDir}/data/bam/reads_mother.bam", @@ -488,7 +482,7 @@ And that's actually all we need to do, because the channel factory we use in the Let's try running the workflow now that the plumbing is set up to run on all three test samples. ```bash -nextflow run hello-genomics.nf -resume +nextflow run genomics-1.nf -resume ``` Funny thing: this _might work_, OR it _might fail_. @@ -497,7 +491,7 @@ If your workflow run succeeded, run it again until you get an error like this: ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `hello-genomics.nf` [loving_pasteur] DSL2 - revision: d2a8e63076 + ┃ Launching `genomics-1.nf` [loving_pasteur] DSL2 - revision: d2a8e63076 executor > local (4) [01/eea165] SAMTOOLS_INDEX (2) | 3 of 3, cached: 1 ✔ @@ -531,14 +525,14 @@ Let's take a look inside the work directory for the failed `GATK_HAPLOTYPECALLER ```console title="Directory contents" work/a5/fa9fd0994b6beede5fb9ea073596c2 -├── intervals.bed -> /workspace/gitpod/hello-nextflow/data/ref/intervals.bed -├── reads_father.bam.bai -> /workspace/gitpod/hello-nextflow/work/01/eea16597bd6e810fb4cf89e60f8c2d/reads_father.bam.bai -├── reads_son.bam -> /workspace/gitpod/hello-nextflow/data/bam/reads_son.bam +├── intervals.bed -> /workspace/gitpod/nf4-science/genomics/data/ref/intervals.bed +├── reads_father.bam.bai -> /workspace/gitpod/nf4-science/genomics/work/01/eea16597bd6e810fb4cf89e60f8c2d/reads_father.bam.bai +├── reads_son.bam -> /workspace/gitpod/nf4-science/genomics/data/bam/reads_son.bam ├── reads_son.bam.vcf ├── reads_son.bam.vcf.idx -├── ref.dict -> /workspace/gitpod/hello-nextflow/data/ref/ref.dict -├── ref.fasta -> /workspace/gitpod/hello-nextflow/data/ref/ref.fasta -└── ref.fasta.fai -> /workspace/gitpod/hello-nextflow/data/ref/ref.fasta.fai +├── ref.dict -> /workspace/gitpod/nf4-science/genomics/data/ref/ref.dict +├── ref.fasta -> /workspace/gitpod/nf4-science/genomics/data/ref/ref.fasta +└── ref.fasta.fai -> /workspace/gitpod/nf4-science/genomics/data/ref/ref.fasta.fai ``` Pay particular attention to the names of the BAM file and the BAM index that are listed in this directory: `reads_son.bam` and `reads_father.bam.bai`. @@ -549,7 +543,7 @@ What the heck? Nextflow has staged an index file in this process call's work dir Add these two lines in the workflow body before the `GATK_HAPLOTYPER` process call: -```groovy title="hello-genomics.nf" linenums="84" +```groovy title="genomics-1.nf" linenums="84" // temporary diagnostics reads_ch.view() SAMTOOLS_INDEX.out.view() @@ -558,7 +552,7 @@ Add these two lines in the workflow body before the `GATK_HAPLOTYPER` process ca Then run the workflow command again. ```bash -nextflow run hello-genomics.nf +nextflow run genomics-1.nf ``` You may need to run it several times for it to fail again. @@ -567,12 +561,12 @@ This error will not reproduce consistently because it is dependent on some varia This is what the output of the two `.view()` calls we added looks like for a failed run: ```console title="Output" -/workspace/gitpod/hello-nextflow/data/bam/reads_mother.bam -/workspace/gitpod/hello-nextflow/data/bam/reads_father.bam -/workspace/gitpod/hello-nextflow/data/bam/reads_son.bam -/workspace/gitpod/hello-nextflow/work/9c/53492e3518447b75363e1cd951be4b/reads_father.bam.bai -/workspace/gitpod/hello-nextflow/work/cc/37894fffdf6cc84c3b0b47f9b536b7/reads_son.bam.bai -/workspace/gitpod/hello-nextflow/work/4d/dff681a3d137ba7d9866e3d9307bd0/reads_mother.bam.bai +/workspace/gitpod/nf4-science/genomics/data/bam/reads_mother.bam +/workspace/gitpod/nf4-science/genomics/data/bam/reads_father.bam +/workspace/gitpod/nf4-science/genomics/data/bam/reads_son.bam +/workspace/gitpod/nf4-science/genomics/work/9c/53492e3518447b75363e1cd951be4b/reads_father.bam.bai +/workspace/gitpod/nf4-science/genomics/work/cc/37894fffdf6cc84c3b0b47f9b536b7/reads_son.bam.bai +/workspace/gitpod/nf4-science/genomics/work/4d/dff681a3d137ba7d9866e3d9307bd0/reads_mother.bam.bai ``` The first three lines correspond to the input channel and the second, to the output channel. @@ -605,14 +599,14 @@ First, let's change the output of the `SAMTOOLS_INDEX` process to include the BA _Before:_ -```groovy title="hello-genomics.nf" linenums="32" +```groovy title="genomics-1.nf" linenums="32" output: path "${input_bam}.bai" ``` _After:_ -```groovy title="hello-genomics.nf" linenums="32" +```groovy title="genomics-1.nf" linenums="32" output: tuple path(input_bam), path("${input_bam}.bai") ``` @@ -627,7 +621,7 @@ Specifically, where we previously declared two separate input paths in the input _Before:_ -```groovy title="hello-genomics.nf" linenums="49" +```groovy title="genomics-1.nf" linenums="49" input: path input_bam path input_bam_index @@ -635,7 +629,7 @@ input: _After:_ -```groovy title="hello-genomics.nf" linenums="49" +```groovy title="genomics-1.nf" linenums="49" input: tuple path(input_bam), path(input_bam_index) ``` @@ -650,7 +644,7 @@ As a result, we can simply delete that line. _Before:_ -```groovy title="hello-genomics.nf" linenums="84" +```groovy title="genomics-1.nf" linenums="84" GATK_HAPLOTYPECALLER( reads_ch, SAMTOOLS_INDEX.out, @@ -658,7 +652,7 @@ GATK_HAPLOTYPECALLER( _After:_ -```groovy title="hello-genomics.nf" linenums="84" +```groovy title="genomics-1.nf" linenums="84" GATK_HAPLOTYPECALLER( SAMTOOLS_INDEX.out, ``` @@ -670,7 +664,7 @@ That is all the re-wiring that is necessary to solve the index mismatch problem. Of course, the proof is in the pudding, so let's run the workflow again a few times to make sure this will work reliably going forward. ```bash -nextflow run hello-genomics.nf +nextflow run genomics-1.nf ``` This time (and every time) everything should run correctly: @@ -678,7 +672,7 @@ This time (and every time) everything should run correctly: ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `hello-genomics.nf` [special_goldstine] DSL2 - revision: 4cbbf6ea3e + ┃ Launching `genomics-1.nf` [special_goldstine] DSL2 - revision: 4cbbf6ea3e executor > local (6) [d6/10c2c4] SAMTOOLS_INDEX (1) | 3 of 3 ✔ @@ -687,7 +681,7 @@ executor > local (6) If you'd like, you can use `.view()` again to peek at what the contents of the `SAMTOOLS_INDEX` output channel looks like: -```groovy title="hello-genomics.nf" linenums="92" +```groovy title="genomics-1.nf" linenums="92" SAMTOOLS_INDEX.out.view() ``` @@ -723,9 +717,9 @@ Here we are going to show you how to do the simple case. We already made a text file listing the input file paths, called `sample_bams.txt`, which you can find in the `data/` directory. ```txt title="sample_bams.txt" -/workspace/gitpod/hello-nextflow/data/bam/reads_mother.bam -/workspace/gitpod/hello-nextflow/data/bam/reads_father.bam -/workspace/gitpod/hello-nextflow/data/bam/reads_son.bam +/workspace/gitpod/nf4-science/genomics/data/bam/reads_mother.bam +/workspace/gitpod/nf4-science/genomics/data/bam/reads_father.bam +/workspace/gitpod/nf4-science/genomics/data/bam/reads_son.bam ``` As you can see, we listed one file path per line, and they are absolute paths. @@ -740,7 +734,7 @@ Let's switch the default value for our `reads_bam` input parameter to point to t _Before:_ -```groovy title="hello-genomics.nf" linenums="7" +```groovy title="genomics-1.nf" linenums="7" // Primary input params.reads_bam = [ "${projectDir}/data/bam/reads_mother.bam", @@ -751,7 +745,7 @@ params.reads_bam = [ _After:_ -```groovy title="hello-genomics.nf" linenums="7" +```groovy title="genomics-1.nf" linenums="7" // Primary input (file of input files, one per line) params.reads_bam = "${projectDir}/data/sample_bams.txt" ``` @@ -767,14 +761,14 @@ Fortunately we can do that very simply, just by adding the [`.splitText()` opera _Before:_ -```groovy title="hello-genomics.nf" linenums="68" +```groovy title="genomics-1.nf" linenums="68" // Create input channel (single file via CLI parameter) reads_ch = Channel.fromPath(params.reads_bam) ``` _After:_ -```groovy title="hello-genomics.nf" linenums="68" +```groovy title="genomics-1.nf" linenums="68" // Create input channel from a text file listing input file paths reads_ch = Channel.fromPath(params.reads_bam).splitText() ``` @@ -788,7 +782,7 @@ reads_ch = Channel.fromPath(params.reads_bam).splitText() Let's run the workflow one more time. ```bash -nextflow run hello-genomics.nf -resume +nextflow run genomics-1.nf -resume ``` This should produce the same result as before, right? @@ -796,7 +790,7 @@ This should produce the same result as before, right? ```console title="Output" N E X T F L O W ~ version 24.10.0 - ┃ Launching `hello-genomics.nf` [sick_albattani] DSL2 - revision: 46d84642f6 + ┃ Launching `genomics-1.nf` [sick_albattani] DSL2 - revision: 46d84642f6 [18/23b4bb] SAMTOOLS_INDEX (1) | 3 of 3, cached: 3 ✔ [12/f727bb] GATK_HAPLOTYPECALLER (3) | 3 of 3, cached: 3 ✔ @@ -808,12 +802,12 @@ And that's it! Our simple variant calling workflow has all the basic features we ### Takeaway -You know how to make a multi-step linear workflow handle a file containing input file paths. +You know how to make a multi-step linear workflow to index a BAM file and apply per-sample variant calling using GATK. -More generally, you've learned how to use essential Nextflow components and logic to build a pipeline that does real work, taking into account the idiosyncrasies of bioinformatics file formats and tool requirements. +More generally, you've learned how to use essential Nextflow components and logic to build a simple genomics pipeline that does real work, taking into account the idiosyncrasies of genomics file formats and tool requirements. ### What's next? Celebrate your success and take an extra long break! -In the next training module, you'll learn how to use a few additional Nextflow features (including more channel operators) to develop pipelines with more complex plumbing. +In the next part of this course, you'll learn how to use a few additional Nextflow features (including more channel operators) to apply joint variant calling to the data. diff --git a/docs/hello_nextflow/05_hello_operators.md b/docs/nf4_science/genomics/02_joint_calling.md similarity index 92% rename from docs/hello_nextflow/05_hello_operators.md rename to docs/nf4_science/genomics/02_joint_calling.md index fcceff174..77ca32353 100644 --- a/docs/hello_nextflow/05_hello_operators.md +++ b/docs/nf4_science/genomics/02_joint_calling.md @@ -1,18 +1,13 @@ -# Part 4: Hello Operators +# Part 2: Joint calling on a cohort -In Part 3, you built a pipeline that was completely linear and processed each sample's data independently of the others. -However, in real pipelines, you may need to combine data from multiple samples, or combine different kinds of data. -Here we show you how to use channels and channel operators to implement a pipeline with more interesting plumbing. +In the first part of this course, you built a variant calling pipeline that was completely linear and processed each sample's data independently of the others. +However, in a real genomics use case, you'll typically need to look at the variant calls of multiple samples together. -Specifically, we show you how to implement joint variant calling with GATK, building on the pipeline from Part 2. - -!!! note - - Don't worry if you're not familiar with GATK or genomics in general. We'll summarize the necessary concepts as we go, and the workflow implementation principles we demonstrate here apply broadly to any use case that follows a similar pattern. +In this second part, we show you how to use channels and channel operators to implement joint variant calling with GATK, building on the pipeline from Part 1. ### Method overview -The GATK variant calling method we used in Part 3 simply generated variant calls per sample. +The GATK variant calling method we used in first part of this course simply generated variant calls per sample. That's fine if you only want to look at the variants from each sample in isolation, but that yields limited information. It's often more interesting to look at how variant calls differ across multiple samples, and to do so, GATK offers an alternative method called joint variant calling, which we demonstrate here. @@ -23,13 +18,15 @@ Joint variant calling involves generating a special kind of variant output calle What's special about a sample's GVCF is that it contains records summarizing sequence data statistics about all positions in the targeted area of the genome, not just the positions where the program found evidence of variation. This is critical for the joint genotyping calculation ([further reading](https://gatk.broadinstitute.org/hc/en-us/articles/360035890431-The-logic-of-joint-calling-for-germline-short-variants)). -The GVCF is produced by GATK HaplotypeCaller, the same tool we used in Part 3, with an additional parameter (`-ERC GVCF`). +The GVCF is produced by GATK HaplotypeCaller, the same tool we used in Part 1, with an additional parameter (`-ERC GVCF`). Combining the GVCFs is done with GATK GenomicsDBImport, which combines the per-sample calls into a data store (analogous to a database), then the actual 'joint genotyping' analysis is done with GATK GenotypeGVCFs. -So to recap, we're going to develop a workflow that does the following: +### Workflow + +So to recap, in this part of the course, we're going to develop a workflow that does the following:
---8<-- "docs/hello_nextflow/img/hello-gatk-2.svg" +--8<-- "docs/nf4_science/genomics/img/hello-gatk-2.svg"
1. Generate an index file for each BAM input file using Samtools @@ -37,12 +34,7 @@ So to recap, we're going to develop a workflow that does the following: 3. Collect all the GVCFs and combine them into a GenomicsDB data store 4. Run joint genotyping on the combined GVCF data store to produce a cohort-level VCF -### Dataset - -- **A reference genome** consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and sequence dictionary). -- **Three whole genome sequencing samples** corresponding to a family trio (mother, father and son), which have been subset to a small portion on chromosome 20 to keep the file sizes small. - The sequencing data is in [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) (Binary Alignment Map) format, _i.e._ genome sequencing reads that have already been mapped to the reference genome. -- **A list of genomic intervals**, _i.e._ coordinates on the genome where our samples have data suitable for calling variants, provided in BED format. +We'll apply this to the same dataset as in Part 1. --- @@ -53,11 +45,11 @@ Just like previously, we want to try out the commands manually before we attempt !!! note Make sure you're in the correct working directory: - `cd /workspace/gitpod/hello-nextflow` + `cd /workspace/gitpod/nf4-science/genomics` ### 0.1. Index a BAM input file with Samtools -This first step is the same as in Part 3: Hello Genomics, so it should feel very familiar, but this time we need to do it for all three samples. +This first step is the same as in Part 1, so it should feel very familiar, but this time we need to do it for all three samples. !!! note @@ -99,7 +91,7 @@ exit ### 0.2. Call variants with GATK HaplotypeCaller in GVCF mode -This second step is very similar to what we did Part 3: Hello Genomics, but we are now going to run GATK in 'GVCF mode'. +This second step is very similar to what we did Part 1: Hello Genomics, but we are now going to run GATK in 'GVCF mode'. #### 0.2.1. Spin up the GATK container interactively @@ -125,7 +117,7 @@ gatk HaplotypeCaller \ This creates the GVCF output file `reads_mother.g.vcf` in the current working directory in the container. -If you `cat` it to view the contents, you'll see it's much longer than the equivalent VCF we generated in Part 3. You can't even scroll up to the start of the file, and most of the lines look quite different from what we saw in the VCF in Part 3. +If you `cat` it to view the contents, you'll see it's much longer than the equivalent VCF we generated in Part 1. You can't even scroll up to the start of the file, and most of the lines look quite different from what we saw in the VCF in Part 1. ```console title="Output" linenums="1674" 20_10037292_10066351 14714 . T . . END=14718 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1192 @@ -143,7 +135,7 @@ In a GVCF, there are typically lots of such non-variant lines, with a smaller nu 20_10037292_10066351 3481 . T . . END=3481 GT:DP:GQ:MIN_DP:PL 0/0:21:51:21:0,51,765 ``` -The second line shows the first variant record in the file, which corresponds to the first variant in the VCF file we looked at in Part 3. +The second line shows the first variant record in the file, which corresponds to the first variant in the VCF file we looked at in Part 1. Just like the original VCF was, the output GVCF file is also accompanied by an index file, called `reads_mother.g.vcf.idx`. @@ -217,7 +209,7 @@ It's another reasonably small file so you can `cat` this file to view its conten 20_10037292_10066351 3529 . T A 154.29 . AC=1;AF=0.167;AN=6;BaseQRankSum=-5.440e-01;DP=104;ExcessHet=0.0000;FS=1.871;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;QD=7.71;ReadPosRankSum=-1.158e+00;SOR=1.034 GT:AD:DP:GQ:PL 0/0:44,0:44:99:0,112,1347 0/1:12,8:20:99:163,0,328 0/0:39,0:39:99:0,105,1194 ``` -This looks more like the original VCF we generated in Part 3, except this time we have genotype-level information for all three samples. +This looks more like the original VCF we generated in Part 1, except this time we have genotype-level information for all three samples. The last three columns in the file are the genotype blocks for the samples, listed in alphabetical order. If we look at the genotypes called for our test family trio for the very first variant, we see that the father is heterozygous-variant (`0/1`), and the mother and son are both homozygous-variant (`1/1`). @@ -232,7 +224,7 @@ exit ### Takeaway -You know how to run the individual commands in the terminal to verify that they will produce the information you want. +You know how to run the individual commands involved in joint variant calling in the terminal to verify that they will produce the information you want. ### What's next? @@ -242,13 +234,13 @@ Wrap these commands into an actual pipeline. ## 1. Modify the per-sample variant calling step to produce a GVCF -The good news is that we don't need to start all over, since we already wrote a workflow that does some of this work in Part 3. +The good news is that we don't need to start all over, since we already wrote a workflow that does some of this work in Part 1. However, that pipeline produces VCF files, whereas now we want GVCF files in order to do the joint genotyping. So we need to start by switching on the GVCF variant calling mode and updating the output file extension. !!! note - For convenience, we are going to work with a fresh copy of the GATK workflow as it stands at the end of Part 3, but under a different name: `hello-operators.nf`. + For convenience, we are going to work with a fresh copy of the GATK workflow as it stands at the end of Part 1, but under a different name: `hello-operators.nf`. ### 1.1. Tell HaplotypeCaller to emit a GVCF and update the output extension @@ -473,7 +465,7 @@ The resulting `all_gvcfs_ch` and `all_idxs_ch` channels are what we're going to !!!note - In case you were wondering, we collect the GVCFs and their index files separately because the GATK GenomicsDBImport command only wants to see the GVCF file paths. Fortunately, since Nextflow will stage all the files together for execution, we don't have to worry about the order of files like we did for BAMs and their index in Part 3. + In case you were wondering, we collect the GVCFs and their index files separately because the GATK GenomicsDBImport command only wants to see the GVCF file paths. Fortunately, since Nextflow will stage all the files together for execution, we don't have to worry about the order of files like we did for BAMs and their index in Part 1. ### 2.4. Add a call to the workflow block to run GATK_GENOMICSDB @@ -844,7 +836,7 @@ You'll find the final output file, `family_trio.joint.vcf` (and its file index), 20_10037292_10066351 3529 . T A 154.29 . AC=1;AF=0.167;AN=6;BaseQRankSum=-5.440e-01;DP=104;ExcessHet=0.0000;FS=1.871;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;QD=7.71;ReadPosRankSum=-1.158e+00;SOR=1.034 GT:AD:DP:GQ:PL 0/0:44,0:44:99:0,112,1347 0/1:12,8:20:99:163,0,328 0/0:39,0:39:99:0,105,1194 ``` -You now have an automated, fully reproducible variant calling workflow! +You now have an automated, fully reproducible joint variant calling workflow! !!!note @@ -860,6 +852,6 @@ You know how to use some common operators as well as Groovy closures to control Celebrate your success and take an extra super mega long break! This was tough and you deserve it. -In the next training, you'll learn how to leverage commonly used workflow configuration options. +When you're ready to move on, have a look at our training portal to browse available training courses and select your next step. **Good luck!** diff --git a/docs/nf4_science/genomics/03_configuration.md b/docs/nf4_science/genomics/03_configuration.md new file mode 100644 index 000000000..485ef6d22 --- /dev/null +++ b/docs/nf4_science/genomics/03_configuration.md @@ -0,0 +1,89 @@ +# Part 3: Resource profiling and optimization + +THIS IS A PLACEHOLDER + +!!!note + + This training module is under redevelopment. + +--- + +TODO + +### 4.3. Run the workflow to generate a resource utilization report + +To have Nextflow generate the report automatically, simply add `-with-report .html` to your command line. + +```bash +nextflow run main.nf -profile my_laptop -with-report report-config-1.html +``` + +The report is an html file, which you can download and open in your browser. You can also right click it in the file explorer on the left and click on `Show preview` in order to view it on Gitpod. + +Take a few minutes to look through the report and see if you can identify some opportunities for adjusting resources. +Make sure to click on the tabs that show the utilization results as a percentage of what was allocated. +There is some [documentation](https://www.nextflow.io/docs/latest/reports.html) describing all the available features. + + + +One observation is that the `GATK_JOINTGENOTYPING` seems to be very hungry for CPU, which makes sense since it performs a lot of complex calculations. +So we could try boosting that and see if it cuts down on runtime. + +However, we seem to have overshot the mark with the memory allocations; all processes are only using a fraction of what we're giving them. +We should dial that back down and save some resources. + +### 4.4. Adjust resource allocations for a specific process + +We can specify resource allocations for a given process using the `withName` process selector. +The syntax looks like this when it's by itself in a process block: + +```groovy title="Syntax" +process { + withName: 'GATK_JOINTGENOTYPING' { + cpus = 4 + } +} +``` + +Let's add that to the existing process block in the `nextflow.config` file. + +```groovy title="nextflow.config" linenums="11" +process { + // defaults for all processes + cpus = 2 + memory = 2.GB + // allocations for a specific process + withName: 'GATK_JOINTGENOTYPING' { + cpus = 4 + } +} +``` + +With that specified, the default settings will apply to all processes **except** the `GATK_JOINTGENOTYPING` process, which is a special snowflake that gets a lot more CPU. +Hopefully that should have an effect. + +### 4.5. Run again with the modified configuration + +Let's run the workflow again with the modified configuration and with the reporting flag turned on, but notice we're giving the report a different name so we can differentiate them. + +```bash +nextflow run main.nf -profile my_laptop -with-report report-config-2.html +``` + +Once again, you probably won't notice a substantial difference in runtime, because this is such a small workload and the tools spend more time in ancillary tasks than in performing the 'real' work. + +However, the second report shows that our resource utilization is more balanced now. + + + +As you can see, this approach is useful when your processes have different resource requirements. It empowers you to right-size the resource allocations you set up for each process based on actual data, not guesswork. + +!!!note + + This is just a tiny taster of what you can do to optimize your use of resources. + Nextflow itself has some really neat [dynamic retry logic](https://training.nextflow.io/basic_training/debugging/#dynamic-resources-allocation) built in to retry jobs that fail due to resource limitations. + Additionally, the Seqera Platform offers AI-driven tooling for optimizing your resource allocations automatically as well. + + We'll cover both of those approaches in an upcoming part of this training course. + +That being said, there may be some constraints on what you can (or must) allocate depending on what computing executor and compute infrastructure you're using. For example, your cluster may require you to stay within certain limits that don't apply when you're running elsewhere. diff --git a/docs/hello_nextflow/08_hello_nf-test.md b/docs/nf4_science/genomics/04_testing.md similarity index 99% rename from docs/hello_nextflow/08_hello_nf-test.md rename to docs/nf4_science/genomics/04_testing.md index 1665d1818..9d1a9ef74 100644 --- a/docs/hello_nextflow/08_hello_nf-test.md +++ b/docs/nf4_science/genomics/04_testing.md @@ -1,4 +1,10 @@ -# Part 7: Hello nf-test +# Part 4: Hello nf-test + +THIS IS A PLACEHOLDER + +!!!note + + This training module is under redevelopment. Being able to systematically test that every part of your workflow is doing what it's supposed to do is critical for reproducibility and long-term maintenance. And it's also helpful during the development process! diff --git a/docs/hello_nextflow/img/gatk-pipeline.png b/docs/nf4_science/genomics/img/gatk-pipeline.png similarity index 100% rename from docs/hello_nextflow/img/gatk-pipeline.png rename to docs/nf4_science/genomics/img/gatk-pipeline.png diff --git a/docs/hello_nextflow/img/haplotype-caller.excalidraw.svg b/docs/nf4_science/genomics/img/haplotype-caller.excalidraw.svg similarity index 100% rename from docs/hello_nextflow/img/haplotype-caller.excalidraw.svg rename to docs/nf4_science/genomics/img/haplotype-caller.excalidraw.svg diff --git a/docs/hello_nextflow/img/hello-gatk-1.svg b/docs/nf4_science/genomics/img/hello-gatk-1.svg similarity index 100% rename from docs/hello_nextflow/img/hello-gatk-1.svg rename to docs/nf4_science/genomics/img/hello-gatk-1.svg diff --git a/docs/hello_nextflow/img/hello-gatk-2.svg b/docs/nf4_science/genomics/img/hello-gatk-2.svg similarity index 100% rename from docs/hello_nextflow/img/hello-gatk-2.svg rename to docs/nf4_science/genomics/img/hello-gatk-2.svg diff --git a/docs/hello_nextflow/img/joint-calling.png b/docs/nf4_science/genomics/img/joint-calling.png similarity index 100% rename from docs/hello_nextflow/img/joint-calling.png rename to docs/nf4_science/genomics/img/joint-calling.png diff --git a/docs/nf4_science/genomics/img/memory-after.png b/docs/nf4_science/genomics/img/memory-after.png new file mode 100644 index 000000000..d61b4a7c5 Binary files /dev/null and b/docs/nf4_science/genomics/img/memory-after.png differ diff --git a/docs/nf4_science/genomics/img/memory-before.png b/docs/nf4_science/genomics/img/memory-before.png new file mode 100644 index 000000000..ce0f7ac27 Binary files /dev/null and b/docs/nf4_science/genomics/img/memory-before.png differ diff --git a/docs/hello_nextflow/img/variants.png b/docs/nf4_science/genomics/img/variants.png similarity index 100% rename from docs/hello_nextflow/img/variants.png rename to docs/nf4_science/genomics/img/variants.png diff --git a/docs/nf4_science/genomics/index.md b/docs/nf4_science/genomics/index.md new file mode 100644 index 000000000..4ae6f3233 --- /dev/null +++ b/docs/nf4_science/genomics/index.md @@ -0,0 +1,48 @@ +--- +title: Nextflow for Genomics +hide: + - toc +--- + +# Nextflow for Genomics + +This training course is intended for researchers in genomics and related fields who are interested in developing or customizing data analysis pipelines. +It builds on the [Hello Nextflow](../hello_nextflow/) beginner training and demonstrates how to use Nextflow in the specific context of the genomics domain. + +Specifically, this course demonstrates how to implement a simple variant calling pipeline with [GATK](https://gatk.broadinstitute.org/) (Genome Analysis Toolkit), a widely used software package for analyzing high-throughput sequencing data. + +!!! note + + Don't worry if you're not familiar with GATK specifically. + We'll summarize the necessary concepts as we go, and the workflow implementation principles we demonstrate here apply broadly to any command line tool that processes genomics data. + +## Learning objectives + +By working through this course, you will learn how to apply foundational Nextflow concepts and tooling to a typical genomics use case. + +By the end of this workshop you will be able to: + +- Write a linear workflow to apply variant calling to a single sample +- Handle accessory files such as index files and reference genome resources appropriately +- Leverage Nextflow's dataflow paradigm to parallelize per-sample variant calling +- Implement multi-sample variant calling using relevant channel operators +- Configure pipeline execution and manage and optimize resource allocations +- Implement per-step and end-to-end pipeline tests that handle genomics-specific idiosyncrasies appropriately + + + +## Prerequisites + +The course assumes some minimal familiarity with the following: + +- Tools and file formats commonly used in this scientific domain +- Experience with the command line +- Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../hello_nextflow/) beginner training. + +For technical requirements and environment setup, see the [Environment Setup](../envsetup/) mini-course. + +## Get started + +To get started, open the training environment by clicking the 'Open in Gitpod' button below. + +[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training) diff --git a/docs/nf4_science/index.md b/docs/nf4_science/index.md new file mode 100644 index 000000000..b8bbdb3d4 --- /dev/null +++ b/docs/nf4_science/index.md @@ -0,0 +1,33 @@ +--- +title: Nextflow for Science +hide: + - toc +--- + +# Nextflow for Science + +These are courses that demonstrate how to apply the concepts and components presented in the [Hello Nextflow](../hello_nextflow/) beginner course to specific scientific use cases. Each course consists of a series of training modules that are designed to help learners build up their skills progressively. + +!!! exercise "Nextflow for Genomics" + + !!! quote inline end "" + + :material-run-fast: Learn to develop a pipeline for genomics in Nextflow. + + This is a course for researchers who wish to learn how to develop their own genomics pipelines. The course uses a variant calling use case to demonstrate how to develop a simple but functional genomics pipeline. + + [Launch the Nextflow for Genomics training :material-arrow-right:](genomics/){ .md-button .md-button--primary } + +**Coming soon:** "Nextflow for RNAseq" — Learn to develop a pipeline for bulk RNAseq analysis in Nextflow + + diff --git a/docs/other/README.md b/docs/other/README.md new file mode 100644 index 000000000..aa353d56a --- /dev/null +++ b/docs/other/README.md @@ -0,0 +1 @@ +This directory contains older training courses that are not actively maintained and that we may repurpose elsewhere or delete in the near future. The corresponding materials are not available within the training environment. You can still find the materials in the GitHub repository and download them for local use. diff --git a/docs/hands_on/01_datasets.md b/docs/other/hands_on/01_datasets.md similarity index 100% rename from docs/hands_on/01_datasets.md rename to docs/other/hands_on/01_datasets.md diff --git a/docs/hands_on/02_workflow.md b/docs/other/hands_on/02_workflow.md similarity index 100% rename from docs/hands_on/02_workflow.md rename to docs/other/hands_on/02_workflow.md diff --git a/docs/hands_on/03_setup.md b/docs/other/hands_on/03_setup.md similarity index 100% rename from docs/hands_on/03_setup.md rename to docs/other/hands_on/03_setup.md diff --git a/docs/hands_on/04_implementation.md b/docs/other/hands_on/04_implementation.md similarity index 100% rename from docs/hands_on/04_implementation.md rename to docs/other/hands_on/04_implementation.md diff --git a/docs/hands_on/index.md b/docs/other/hands_on/index.md similarity index 100% rename from docs/hands_on/index.md rename to 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Docs currently in here are stubs based on content recycled from elsewhere. diff --git a/docs/side_quests/containers.md b/docs/side_quests/containers.md new file mode 100644 index 000000000..ff62a0bba --- /dev/null +++ b/docs/side_quests/containers.md @@ -0,0 +1,189 @@ +# Part 1: More Containers + +[TODO] + +--- + +## 1. How to find or make container images + +Some software developers provide container images for their software that are available on container registries like Docker Hub, but many do not. +In this optional section, we'll show you to two ways to get a container image for tools you want to use in your Nextflow pipelines: using Seqera Containers and building the container image yourself. + +You'll be getting/building a container image for the `quote` pip package, which will be used in the exercise at the end of this section. + +### 1.1. Get a container image from Seqera Containers + +Seqera Containers is a free service that builds container images for pip and conda (including bioconda) installable tools. +Navigate to [Seqera Containers](https://www.seqera.io/containers/) and search for the `quote` pip package. + +![Seqera Containers](img/seqera-containers-1.png) + +Click on "+Add" and then "Get Container" to request a container image for the `quote` pip package. + +![Seqera Containers](img/seqera-containers-2.png) + +If this is the first time a community container has been built for this version of the package, it may take a few minutes to complete. +Click to copy the URI (e.g. `community.wave.seqera.io/library/pip_quote:ae07804021465ee9`) of the container image that was created for you. + +You can now use the container image to run the `quote` command and get a random saying from Grace Hopper. + +```bash +docker run --rm community.wave.seqera.io/library/pip_quote:ae07804021465ee9 quote "Grace Hopper" +``` + +Output: + +```console title="Output" +Humans are allergic to change. They love to say, 'We've always done it +this way.' I try to fight that. That's why I have a clock on my wall +that runs counter-clockwise. +``` + +### 1.2. Build the container image yourself + +Let's use some build details from the Seqera Containers website to build the container image for the `quote` pip package ourselves. +Return to the Seqera Containers website and click on the "Build Details" button. + +The first item we'll look at is the `Dockerfile`, a type of script file that contains all the commands needed to build the container image. +We've added some explanatory comments to the Dockerfile below to help you understand what each part does. + +```Dockerfile title="Dockerfile" +# Start from the micromamba base docker image +FROM mambaorg/micromamba:1.5.10-noble +# Copy the conda.yml file into the container +COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml +# Install various utilities for Nextflow to use and the packages in the conda.yml file +RUN micromamba install -y -n base -f /tmp/conda.yml \ + && micromamba install -y -n base conda-forge::procps-ng \ + && micromamba env export --name base --explicit > environment.lock \ + && echo ">> CONDA_LOCK_START" \ + && cat environment.lock \ + && echo "<< CONDA_LOCK_END" \ + && micromamba clean -a -y +# Run the container as the root user +USER root +# Set the PATH environment variable to include the micromamba installation directory +ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH" +``` + +The second item we'll look at is the `conda.yml` file, which contains the list of packages that need to be installed in the container image. + +```conda.yml title="conda.yml" +channels: +- conda-forge +- bioconda +dependencies: +- pip +- pip: + - quote==3.0.0 # +``` + +Copy the contents of these files into the stubs located in the `containers/build` directory, then run the following command to build the container image yourself. + +!!! Note + + We use the `-t quote:latest` flag to tag the container image with the name `quote` and the tag `latest`. + We will be able to use this tag to refer to the container image when running it on this system. + +```bash +docker build -t quote:latest containers/build +``` + +After it has finished building, you can run the container image you just built. + +```bash +docker run --rm quote:latest quote "Margaret Oakley Dayhoff" +``` + +### Takeaway + +You've learned two different ways to get a container image for a tool you want to use in your Nextflow pipelines: using Seqera Containers and building the container image yourself. + +### What's next? + +You have everything you need to continue to the [next chapter](./04_hello_genomics.md) of this training series. +You can also continue on with an optional exercise to fetch quotes on computer/biology pioneers using the `quote` container and output them using the `cowsay` container. + +--- + +## 2. Make the cow quote famous scientists + +This section contains some stretch exercises, to practice what you've learned so far. +Doing these exercises is _not required_ to understand later parts of the training, but provide a fun way to reinforce your learnings by figuring out how to make the cow quote famous scientists. + +```console title="cowsay-output-Grace-Hopper.txt" + _________________________________________________ + / \ +| Humans are allergic to change. They love to | +| say, 'We've always done it this way.' I try to fi | +| ght that. That's why I have a clock on my wall th | +| at runs counter-clockwise. | +| -Grace Hopper | + \ / + ================================================= + \ + \ + ^__^ + (oo)\_______ + (__)\ )\/\ + ||----w | + || || +``` + +### 2.1. Modify the `hello-containers.nf` script to use a getQuote process + +We have a list of computer and biology pioneers in the `containers/data/pioneers.csv` file. +At a high level, to complete this exercise you will need to: + +- Modify the default `params.input_file` to point to the `pioneers.csv` file. +- Create a `getQuote` process that uses the `quote` container to fetch a quote for each input. +- Connect the output of the `getQuote` process to the `cowsay` process to display the quote. + +For the `quote` container image, you can either use the one you built yourself in the previous stretch exercise or use the one you got from Seqera Containers . + +!!! Hint + + A good choice for the `script` block of your getQuote process might be: + ```groovy + script: + def safe_author = author.tokenize(' ').join('-') + """ + quote "$author" > quote-${safe_author}.txt + echo "-${author}" >> quote-${safe_author}.txt + """ + ``` + +You can find a solution to this exercise in `containers/solutions/hello-containers-4.1.nf`. + +### 2.2. Modify your Nextflow pipeline to allow it to execute in `quote` and `sayHello` modes. + +Add some branching logic using to your pipeline to allow it to accept inputs intended for both `quote` and `sayHello`. +Here's an example of how to use an `if` statement in a Nextflow workflow: + +```groovy title="hello-containers.nf" +workflow { + if (params.quote) { + ... + } + else { + ... + } + cowSay(text_ch) +} +``` + +!!! Hint + + You can use `new_ch = processName.out` to assign a name to the output channel of a process. + +You can find a solution to this exercise in `containers/solutions/hello-containers-4.2.nf`. + +### Takeaway + +You know how to use containers in Nextflow to run processes, and how to build some branching logic into your pipelines! + +### What's next? + +Celebrate, take a stretch break and drink some water! + +When you are ready, move on to Part 3 of this training series to learn how to apply what you've learned so far to a more realistic data analysis use case. diff --git a/docs/side_quests/if_else.md b/docs/side_quests/if_else.md new file mode 100644 index 000000000..62bb74853 --- /dev/null +++ b/docs/side_quests/if_else.md @@ -0,0 +1,87 @@ +# Part 2: If - Else + +[TODO] + +--- + +## 1. Make the cow quote famous scientists + +This section contains some stretch exercises, to practice what you've learned so far. +Doing these exercises is _not required_ to understand later parts of the training, but provide a fun way to reinforce your learnings by figuring out how to make the cow quote famous scientists. + +```console title="cowsay-output-Grace-Hopper.txt" + _________________________________________________ + / \ +| Humans are allergic to change. They love to | +| say, 'We've always done it this way.' I try to fi | +| ght that. That's why I have a clock on my wall th | +| at runs counter-clockwise. | +| -Grace Hopper | + \ / + ================================================= + \ + \ + ^__^ + (oo)\_______ + (__)\ )\/\ + ||----w | + || || +``` + +### 1.1. Modify the `hello-containers.nf` script to use a getQuote process + +We have a list of computer and biology pioneers in the `containers/data/pioneers.csv` file. +At a high level, to complete this exercise you will need to: + +- Modify the default `params.input_file` to point to the `pioneers.csv` file. +- Create a `getQuote` process that uses the `quote` container to fetch a quote for each input. +- Connect the output of the `getQuote` process to the `cowsay` process to display the quote. + +For the `quote` container image, you can either use the one you built yourself in the previous stretch exercise or use the one you got from Seqera Containers . + +!!! Hint + + A good choice for the `script` block of your getQuote process might be: + ```groovy + script: + def safe_author = author.tokenize(' ').join('-') + """ + quote "$author" > quote-${safe_author}.txt + echo "-${author}" >> quote-${safe_author}.txt + """ + ``` + +You can find a solution to this exercise in `containers/solutions/hello-containers-4.1.nf`. + +### 1.2. Modify your Nextflow pipeline to allow it to execute in `quote` and `sayHello` modes. + +Add some branching logic using to your pipeline to allow it to accept inputs intended for both `quote` and `sayHello`. +Here's an example of how to use an `if` statement in a Nextflow workflow: + +```groovy title="hello-containers.nf" +workflow { + if (params.quote) { + ... + } + else { + ... + } + cowSay(text_ch) +} +``` + +!!! Hint + + You can use `new_ch = processName.out` to assign a name to the output channel of a process. + +You can find a solution to this exercise in `containers/solutions/hello-containers-4.2.nf`. + +### Takeaway + +You know how to use containers in Nextflow to run processes, and how to build some branching logic into your pipelines! + +### What's next? + +Celebrate, take a stretch break and drink some water! + +When you are ready, move on to Part 3 of this training series to learn how to apply what you've learned so far to a more realistic data analysis use case. diff --git a/docs/side_quests/index.md b/docs/side_quests/index.md new file mode 100644 index 000000000..16e484e91 --- /dev/null +++ b/docs/side_quests/index.md @@ -0,0 +1,27 @@ +--- +title: Side Quests +hide: + - toc +--- + +# Side Quests + +[TODO] This is a collection of standalone training modules that go deeper into specific topics. You can go through them in any order. + +Let's get started! + +[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training) + +## Learning objectives + +The learning objectives are specific to each section. [TODO] + +## Audience & prerequisites + +[TODO] + +**Prerequisites** + +- A GitHub account +- Experience with command line + [TODO] diff --git a/docs/side_quests/orientation.md b/docs/side_quests/orientation.md new file mode 100644 index 000000000..4a2047847 --- /dev/null +++ b/docs/side_quests/orientation.md @@ -0,0 +1,46 @@ +# Orientation + +The Gitpod environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. +However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface. + +If you have not yet done so, please follow [this link](../../envsetup/) before going any further. + +## Materials provided + +Throughout this training course, we'll be working in the `tapas/` directory. +This directory contains all the code files, test data and accessory files you will need. + +Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the Gitpod workspace. +Alternatively, you can use the `tree` command. +Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity. + +Here we generate a table of contents to the second level down: + +```bash +tree . -L 2 +``` + +If you run this inside `tapas`, you should see the following output: [TODO] + +```console title="Directory contents" +. +``` + +!!!note + + Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course. + This is just meant to give you an overview. + +**Here's a summary of what you should know to get started:** + +[TODO] + +!!!tip + + If for whatever reason you move out of this directory, you can always run this command to return to it: + + ```bash + cd /workspace/gitpod/tapas + ``` + +Now, to begin the course, click on the arrow in the bottom right corner of this page. diff --git a/gitpod-ws.code-workspace b/gitpod-ws.code-workspace index eac21106c..f6865101f 100644 --- a/gitpod-ws.code-workspace +++ b/gitpod-ws.code-workspace @@ -1,11 +1,9 @@ { "folders": [ { "path": "./hello-nextflow" }, + { "path": "./nf4-science" }, { "path": "./nf-training" }, { "path": "./nf-training-advanced" }, - { "path": "./nf-customize" }, - { "path": "./nf-develop" }, - { "path": "./troubleshoot" }, ], "settings": { "typescript.tsdk": "gitpod/node_modules/typescript/lib", diff --git a/hello-nextflow/containers/build/Dockerfile b/hello-nextflow/containers/build/Dockerfile deleted file mode 100644 index e69de29bb..000000000 diff --git a/hello-nextflow/containers/build/conda.yml b/hello-nextflow/containers/build/conda.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/hello-nextflow/containers/data/greetings.csv b/hello-nextflow/containers/data/greetings.csv deleted file mode 100644 index ab8a5901d..000000000 --- a/hello-nextflow/containers/data/greetings.csv +++ /dev/null @@ -1 +0,0 @@ -Hello,Bonjour,Holà diff --git a/hello-nextflow/containers/data/pioneers.csv b/hello-nextflow/containers/data/pioneers.csv deleted file mode 100644 index d97928012..000000000 --- a/hello-nextflow/containers/data/pioneers.csv +++ /dev/null @@ -1,4 +0,0 @@ -Grace Hopper -Alan Turing -Margaret Oakley Dayhoff -Rosalind Franklin diff --git a/hello-nextflow/containers/results/.gitignore b/hello-nextflow/containers/results/.gitignore deleted file mode 100644 index d6b7ef32c..000000000 --- a/hello-nextflow/containers/results/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -* -!.gitignore diff --git a/hello-nextflow/containers/solutions/hello-containers-3.nf b/hello-nextflow/containers/solutions/hello-containers-3.nf deleted file mode 100644 index cdefb478d..000000000 --- a/hello-nextflow/containers/solutions/hello-containers-3.nf +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ -params.input_file = "containers/data/greetings.csv" -// params.character can be any of 'beavis', 'cheese', 'cow', 'daemon', 'dragon', 'fox', 'ghostbusters', 'kitty', -// 'meow', 'miki', 'milk', 'octopus', 'pig', 'stegosaurus', 'stimpy', 'trex', 'turkey', 'turtle', 'tux' -params.character = "cow" - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - publishDir 'containers/results', mode: 'copy' - - input: - val greeting - - output: - path "output-*.txt" - - script: - // Replace the spaces in the greeting with hyphens for the output filename - def safe_greeting = greeting.tokenize(' ').join('-') - """ - echo '$greeting' > 'output-${safe_greeting}.txt' - """ -} - -/* - * Use a cow (or other character) to say some text - */ -process cowSay { - - publishDir 'containers/results', mode: 'copy' - container 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' - - input: - path input_file - - output: - path "cowsay-*" - - script: - """ - cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file} - """ -} - -workflow { - - // create a channel for inputs from a CSV file - input_ch = Channel.fromPath(params.input_file) - .splitCsv() - .flatten() - - sayHello(input_ch) - - // cowSay the text - cowSay(sayHello.out) -} diff --git a/hello-nextflow/containers/solutions/hello-containers-4.1.nf b/hello-nextflow/containers/solutions/hello-containers-4.1.nf deleted file mode 100644 index fc2e9ba7f..000000000 --- a/hello-nextflow/containers/solutions/hello-containers-4.1.nf +++ /dev/null @@ -1,83 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ -params.input_file = "containers/data/pioneers.csv" -// params.character can be any of 'beavis', 'cheese', 'cow', 'daemon', 'dragon', 'fox', 'ghostbusters', 'kitty', -// 'meow', 'miki', 'milk', 'octopus', 'pig', 'stegosaurus', 'stimpy', 'trex', 'turkey', 'turtle', 'tux' -params.character = "cow" - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - publishDir 'containers/results', mode: 'copy' - - input: - val greeting - - output: - path "output-*.txt" - - script: - // Replace the spaces in the greeting with hyphens for the output filename - def safe_greeting = greeting.tokenize(' ').join('-') - """ - echo '$greeting' > 'output-${safe_greeting}.txt' - """ -} - -/* - * Use a cow (or other character) to say some text - */ -process cowSay { - - publishDir 'containers/results', mode: 'copy' - container 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' - - input: - path input_file - - output: - path "cowsay-*" - - script: - """ - cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file} - """ -} - -process getQuote { - - publishDir 'containers/results', mode: 'copy' - container 'community.wave.seqera.io/library/pip_quote:ae07804021465ee9' - - input: - val author - - output: - path "quote-*.txt" - - script: - // Replace the spaces in the author with hyphens for the output filename - def safe_author = author.tokenize(' ').join('-') - """ - quote "$author" > quote-${safe_author}.txt - echo "-${author}" >> quote-${safe_author}.txt - """ -} - -workflow { - - // create a channel for inputs from a CSV file - input_ch = Channel.fromPath(params.input_file) - .splitCsv() - .flatten() - - getQuote(input_ch) - - // cowSay the text - cowSay(getQuote.out) -} diff --git a/hello-nextflow/containers/solutions/hello-containers-4.2.nf b/hello-nextflow/containers/solutions/hello-containers-4.2.nf deleted file mode 100644 index 9a38316c8..000000000 --- a/hello-nextflow/containers/solutions/hello-containers-4.2.nf +++ /dev/null @@ -1,94 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ -params.input_file = "containers/data/pioneers.csv" -params.quote = true -// params.character can be any of 'beavis', 'cheese', 'cow', 'daemon', 'dragon', 'fox', 'ghostbusters', 'kitty', -// 'meow', 'miki', 'milk', 'octopus', 'pig', 'stegosaurus', 'stimpy', 'trex', 'turkey', 'turtle', 'tux' -params.character = "cow" - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - publishDir 'containers/results', mode: 'copy' - - input: - val greeting - - output: - path "output-*.txt" - - script: - // Replace the spaces in the greeting with hyphens for the output filename - def safe_greeting = greeting.tokenize(' ').join('-') - """ - echo '$greeting' > 'output-${safe_greeting}.txt' - """ -} - -/* - * Use a cow (or other character) to say some text - */ -process cowSay { - - publishDir 'containers/results', mode: 'copy' - container 'community.wave.seqera.io/library/pip_cowsay:131d6a1b707a8e65' - - input: - path input_file - - output: - path "cowsay-*" - - script: - """ - cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file} - """ -} - -/* - * Get a quote by author name from the goodreads API - */ -process getQuote { - - publishDir 'containers/results', mode: 'copy' - container 'community.wave.seqera.io/library/pip_quote:ae07804021465ee9' - - input: - val author - - output: - path "quote-*.txt" - - script: - // Replace the spaces in the author with hyphens for the output filename - def safe_author = author.tokenize(' ').join('-') - """ - quote "$author" > quote-${safe_author}.txt - echo "-${author}" >> quote-${safe_author}.txt - """ -} - -workflow { - - // create a channel for inputs from a CSV file - input_ch = Channel.fromPath(params.input_file) - .splitCsv() - .flatten() - - // create a channel for the text to be processed - if (params.quote) { - getQuote(input_ch) - text_ch = getQuote.out - } else { - sayHello(input_ch) - text_ch = sayHello.out - } - - // cowSay the text - cowSay(text_ch) -} diff --git a/hello-nextflow/data/greetings.csv b/hello-nextflow/data/greetings.csv deleted file mode 100644 index ab8a5901d..000000000 --- a/hello-nextflow/data/greetings.csv +++ /dev/null @@ -1 +0,0 @@ -Hello,Bonjour,Holà diff --git a/hello-nextflow/data/sample_bams.txt b/hello-nextflow/data/sample_bams.txt deleted file mode 100644 index 64e2ce928..000000000 --- a/hello-nextflow/data/sample_bams.txt +++ /dev/null @@ -1,3 +0,0 @@ -/workspace/gitpod/hello-nextflow/data/bam/reads_mother.bam -/workspace/gitpod/hello-nextflow/data/bam/reads_father.bam -/workspace/gitpod/hello-nextflow/data/bam/reads_son.bam diff --git a/hello-nextflow/data/samplesheet.csv b/hello-nextflow/data/samplesheet.csv deleted file mode 100644 index 17fb15a46..000000000 --- a/hello-nextflow/data/samplesheet.csv +++ /dev/null @@ -1,4 +0,0 @@ -id,reads_bam -NA12878,/workspace/gitpod/hello-nextflow/data/bam/reads_mother.bam -NA12877,/workspace/gitpod/hello-nextflow/data/bam/reads_father.bam -NA12882,/workspace/gitpod/hello-nextflow/data/bam/reads_son.bam diff --git a/hello-nextflow/greetings.csv b/hello-nextflow/greetings.csv new file mode 100644 index 000000000..c5889e19a --- /dev/null +++ b/hello-nextflow/greetings.csv @@ -0,0 +1,3 @@ +Hello +Bonjour +Holà diff --git a/hello-nextflow/hello-channels.nf b/hello-nextflow/hello-channels.nf new file mode 100644 index 000000000..6236eea21 --- /dev/null +++ b/hello-nextflow/hello-channels.nf @@ -0,0 +1,31 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path 'output.txt' + + script: + """ + echo '$greeting' > output.txt + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'Holà mundo!' + +workflow { + + // emit a greeting + sayHello(params.greeting) +} diff --git a/hello-nextflow/hello-config.nf b/hello-nextflow/hello-config.nf new file mode 100644 index 000000000..f187831d1 --- /dev/null +++ b/hello-nextflow/hello-config.nf @@ -0,0 +1,37 @@ +#!/usr/bin/env nextflow + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' +params.character = 'turkey' + +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' +include { collectGreetings } from './modules/collectGreetings.nf' +include { cowpy } from './modules/cowpy.nf' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } + + // generate ASCII art of the greetings with cowpy + cowpy(collectGreetings.out.outfile, params.character) +} diff --git a/hello-nextflow/hello-config/demo-params.json b/hello-nextflow/hello-config/demo-params.json deleted file mode 100644 index 59be1e1d4..000000000 --- a/hello-nextflow/hello-config/demo-params.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "reads_bam": "data/sample_bams.txt", - "outdir": "results_genomics", - "reference": "data/ref/ref.fasta", - "reference_index": "data/ref/ref.fasta.fai", - "reference_dict": "data/ref/ref.dict", - "intervals": "data/ref/intervals.bed", - "cohort_name": "family_trio" -} diff --git a/hello-nextflow/hello-config/main.nf b/hello-nextflow/hello-config/main.nf deleted file mode 100644 index 755b55455..000000000 --- a/hello-nextflow/hello-config/main.nf +++ /dev/null @@ -1,149 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input (file of input files, one per line) -params.reads_bam = "${projectDir}/data/sample_bams.txt" - -// Output directory -params.outdir = "results_genomics" - -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -// Base name for final output file -params.cohort_name = "family_trio" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} - -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" - path "${cohort_name}.joint.vcf.idx" - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) - - // Collect variant calling outputs across samples - all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect() - all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect() - - // Combine GVCFs into a GenomicsDB data store and apply joint genotyping - GATK_JOINTGENOTYPING( - all_gvcfs_ch, - all_idxs_ch, - intervals_file, - params.cohort_name, - ref_file, - ref_index_file, - ref_dict_file - ) -} diff --git a/hello-nextflow/hello-config/nextflow.config b/hello-nextflow/hello-config/nextflow.config deleted file mode 100644 index 187d8f216..000000000 --- a/hello-nextflow/hello-config/nextflow.config +++ /dev/null @@ -1,2 +0,0 @@ -docker.fixOwnership = true -docker.enabled = true diff --git a/hello-nextflow/hello-containers.nf b/hello-nextflow/hello-containers.nf index fa799b78b..8764606bf 100644 --- a/hello-nextflow/hello-containers.nf +++ b/hello-nextflow/hello-containers.nf @@ -3,60 +3,30 @@ /* * Pipeline parameters */ -params.input_file = "containers/data/greetings.csv" -// params.character can be any of 'beavis', 'cheese', 'cow', 'daemon', 'dragon', 'fox', 'ghostbusters', 'kitty', -// 'meow', 'miki', 'milk', 'octopus', 'pig', 'stegosaurus', 'stimpy', 'trex', 'turkey', 'turtle', 'tux' -params.character = "cow" +params.greeting = 'greetings.csv' +params.batch = 'test-batch' -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - publishDir 'containers/results', mode: 'copy' - - input: - val greeting - - output: - path "output-*.txt" - - script: - // Replace the spaces in the greeting with hyphens for the output filename - def safe_greeting = greeting.tokenize(' ').join('-') - """ - echo '$greeting' > 'output-${safe_greeting}.txt' - """ -} - -/* - * Use a cow (or other character) to say some text - */ -process cowSay { - - publishDir 'containers/results', mode: 'copy' - - input: - path input_file - - output: - path "cowsay-*" - - script: - """ - cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file} - """ -} +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' +include { collectGreetings } from './modules/collectGreetings.nf' workflow { // create a channel for inputs from a CSV file - input_ch = Channel.fromPath(params.input_file) - .splitCsv() - .flatten() + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) - sayHello(input_ch) + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) - // cowSay the text - cowSay(sayHello.out) + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } } diff --git a/hello-nextflow/hello-modules.nf b/hello-nextflow/hello-modules.nf new file mode 100644 index 000000000..ccf29abd6 --- /dev/null +++ b/hello-nextflow/hello-modules.nf @@ -0,0 +1,87 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} + +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} + +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + val batch_name + + output: + path "COLLECTED-${batch_name}-output.txt" , emit: outfile + val count_greetings , emit: count + + script: + count_greetings = input_files.size() + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } +} diff --git a/hello-nextflow/hello-modules/demo-params.json b/hello-nextflow/hello-modules/demo-params.json deleted file mode 100644 index 59be1e1d4..000000000 --- a/hello-nextflow/hello-modules/demo-params.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "reads_bam": "data/sample_bams.txt", - "outdir": "results_genomics", - "reference": "data/ref/ref.fasta", - "reference_index": "data/ref/ref.fasta.fai", - "reference_dict": "data/ref/ref.dict", - "intervals": "data/ref/intervals.bed", - "cohort_name": "family_trio" -} diff --git a/hello-nextflow/hello-modules/main.nf b/hello-nextflow/hello-modules/main.nf deleted file mode 100644 index 316b0c3a8..000000000 --- a/hello-nextflow/hello-modules/main.nf +++ /dev/null @@ -1,133 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - conda "bioconda::samtools=1.20" - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} - -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" - path "${cohort_name}.joint.vcf.idx" - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) - - // Collect variant calling outputs across samples - all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect() - all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect() - - // Combine GVCFs into a GenomicsDB data store and apply joint genotyping - GATK_JOINTGENOTYPING( - all_gvcfs_ch, - all_idxs_ch, - intervals_file, - params.cohort_name, - ref_file, - ref_index_file, - ref_dict_file - ) -} diff --git a/hello-nextflow/hello-modules/nextflow.config b/hello-nextflow/hello-modules/nextflow.config deleted file mode 100644 index 86142d64b..000000000 --- a/hello-nextflow/hello-modules/nextflow.config +++ /dev/null @@ -1,70 +0,0 @@ -docker.fixOwnership = true - -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = null - - // Output directory - params.outdir = "results_genomics" - - // Accessory files - reference = null - reference_index = null - reference_dict = null - intervals = null - - // Base name for final output file - cohort_name = "my_cohort" -} - -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - my_laptop { - process.executor = 'local' - docker.enabled = true - } - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - process.resourceLimits = [ - memory: 750.GB, - cpus: 200, - time: 30.d - ] - } - demo { - // Primary input (file of input files, one per line) - params.reads_bam = "data/sample_bams.txt" - - // Output directory - params.outdir = "results_genomics" - - // Accessory files - params.reference = "data/ref/ref.fasta" - params.reference_index = "data/ref/ref.fasta.fai" - params.reference_dict = "data/ref/ref.dict" - params.intervals = "data/ref/intervals.bed" - - // Base name for final output file - params.cohort_name = "family_trio" - } -} - -process { - // defaults for all processes - cpus = 2 - memory = 2.GB - // allocations for a specific process - withName: 'GATK_JOINTGENOTYPING' { - cpus = 4 - } -} diff --git a/hello-nextflow/hello-nf-core/data/sequencer_samplesheet.csv b/hello-nextflow/hello-nf-core/data/sequencer_samplesheet.csv deleted file mode 100644 index f2c3b7805..000000000 --- a/hello-nextflow/hello-nf-core/data/sequencer_samplesheet.csv +++ /dev/null @@ -1,5 +0,0 @@ -sample,sequencer,fastq_1,fastq_2 -SAMPLE1_PE,sequencer1,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz -SAMPLE2_PE,sequencer2,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz -SAMPLE3_SE,sequencer3,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz, -SAMPLE3_SE,sequencer3,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz, diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.editorconfig b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.editorconfig deleted file mode 100644 index 72dda289a..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.editorconfig +++ /dev/null @@ -1,33 +0,0 @@ -root = true - -[*] -charset = utf-8 -end_of_line = lf -insert_final_newline = true -trim_trailing_whitespace = true -indent_size = 4 -indent_style = space - -[*.{md,yml,yaml,html,css,scss,js}] -indent_size = 2 - -# These files are edited and tested upstream in nf-core/modules -[/modules/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset -[/subworkflows/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset - -[/assets/email*] -indent_size = unset - -# ignore python and markdown -[*.{py,md}] -indent_style = unset diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.nf-core.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.nf-core.yml deleted file mode 100644 index be6f132c5..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.nf-core.yml +++ /dev/null @@ -1,104 +0,0 @@ -bump_version: null -lint: - 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- docs/images/nf-core-myfirstpipeline_logo_dark.png - - .github/ISSUE_TEMPLATE/bug_report.yml - multiqc_config: - - report_comment - nextflow_config: - - manifest.name - - manifest.homePage - - validation.help.beforeText - - validation.help.afterText - - validation.summary.beforeText - - validation.summary.afterText - readme: - - nextflow_badge - - nextflow_badge - - nextflow_badge -nf_core_version: 3.0.2 -org_path: null -repository_type: pipeline -template: - author: gitpod - description: My first pipeline - force: true - is_nfcore: false - name: myfirstpipeline - org: myorg - outdir: . - skip_features: - - github - - ci - - igenomes - - github_badges - - citations - - gitpod - - codespaces - - fastqc - - changelog - - adaptivecard - - slackreport - version: 1.0.0dev -update: null diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.pre-commit-config.yaml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.pre-commit-config.yaml deleted file mode 100644 index 9e9f0e1c4..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.pre-commit-config.yaml +++ /dev/null @@ -1,13 +0,0 @@ -repos: - - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v3.1.0" - hooks: - - id: prettier - additional_dependencies: - - prettier@3.2.5 - - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.0.3" - hooks: - - id: editorconfig-checker - alias: ec diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierignore b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierignore deleted file mode 100644 index e702cf0b9..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierignore +++ /dev/null @@ -1,10 +0,0 @@ -email_template.html -.nextflow* -work/ -data/ -results/ -.DS_Store -testing/ -testing* -*.pyc -bin/ diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierrc.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierrc.yml deleted file mode 100644 index c81f9a766..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierrc.yml +++ /dev/null @@ -1 +0,0 @@ -printWidth: 120 diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/LICENSE b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/LICENSE deleted file mode 100644 index 6f6f81482..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) gitpod - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/README.md b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/README.md deleted file mode 100644 index 7c215977b..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/README.md +++ /dev/null @@ -1,77 +0,0 @@ -# myorg/myfirstpipeline - -## Introduction - -**myorg/myfirstpipeline** is a bioinformatics pipeline that ... - - - - - - -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) - -## Usage - -> [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - - - -Now, you can run the pipeline using: - - - -```bash -nextflow run myorg/myfirstpipeline \ - -profile \ - --input samplesheet.csv \ - --outdir -``` - -> [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). - -## Credits - -myorg/myfirstpipeline was originally written by gitpod. - -We thank the following people for their extensive assistance in the development of this pipeline: - - - -## Contributions and Support - -If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). - -## Citations - - - - -This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE). - -> **The nf-core framework for community-curated bioinformatics pipelines.** -> -> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. -> -> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.html b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.html deleted file mode 100644 index 68fe28ceb..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.html +++ /dev/null @@ -1,110 +0,0 @@ - - - - - - - - myorg/myfirstpipeline Pipeline Report - - -
- - -

myorg/myfirstpipeline ${version}

-

Run Name: $runName

- - <% if (!success){ out << """ -
-

myorg/myfirstpipeline execution completed unsuccessfully!

-

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

-

The full error message was:

- 
${errorReport}
-
- """ } else { out << """ -
- myorg/myfirstpipeline execution completed successfully! -
- """ } %> - -

The workflow was completed at $dateComplete (duration: $duration)

-

The command used to launch the workflow was as follows:

- 
-$commandLine
- -

Pipeline Configuration:

- - - <% out << summary.collect{ k,v -> " - - - - - " }.join("\n") %> - -
- $k - - 
$v
-
- -

myorg/myfirstpipeline

-

https://github.com/myorg/myfirstpipeline

-
- - diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.txt b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.txt deleted file mode 100644 index 03310b67d..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.txt +++ /dev/null @@ -1,31 +0,0 @@ -Run Name: $runName - -<% if (success){ - out << "## myorg/myfirstpipeline execution completed successfully! ##" -} else { - out << """#################################################### -## myorg/myfirstpipeline execution completed unsuccessfully! ## -#################################################### -The exit status of the task that caused the workflow execution to fail was: $exitStatus. -The full error message was: - -${errorReport} -""" -} %> - - -The workflow was completed at $dateComplete (duration: $duration) - -The command used to launch the workflow was as follows: - - $commandLine - - - -Pipeline Configuration: ------------------------ -<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> - --- -myorg/myfirstpipeline -https://github.com/myorg/myfirstpipeline diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/multiqc_config.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/multiqc_config.yml deleted file mode 100644 index 2306d17cf..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/multiqc_config.yml +++ /dev/null @@ -1,14 +0,0 @@ -report_comment: > - This report has been generated by the myorg/myfirstpipeline - analysis pipeline. -report_section_order: - "myorg-myfirstpipeline-methods-description": - order: -1000 - software_versions: - order: -1001 - "myorg-myfirstpipeline-summary": - order: -1002 - -export_plots: true - -disable_version_detection: true diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/samplesheet.csv b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/samplesheet.csv deleted file mode 100644 index 5f653ab7b..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/samplesheet.csv +++ /dev/null @@ -1,3 +0,0 @@ -sample,fastq_1,fastq_2 -SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz -SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/schema_input.json b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/schema_input.json deleted file mode 100644 index ab54904b1..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/schema_input.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/myorg/myfirstpipeline/master/assets/schema_input.json", - "title": "myorg/myfirstpipeline pipeline - params.input schema", - "description": "Schema for the file provided with params.input", - "type": "array", - "items": { - "type": "object", - "properties": { - "sample": { - "type": "string", - "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces", - "meta": ["id"] - }, - "sequencer": { - "type": "string", - "pattern": "^\\S+$", - "meta": ["sequencer"] - }, - "fastq_1": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" - }, - "fastq_2": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" - } - }, - "required": ["sample", "fastq_1"] - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/sendmail_template.txt b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/sendmail_template.txt deleted file mode 100644 index 6fd27c517..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/sendmail_template.txt +++ /dev/null @@ -1,53 +0,0 @@ -To: $email -Subject: $subject -Mime-Version: 1.0 -Content-Type: multipart/related;boundary="nfcoremimeboundary" - ---nfcoremimeboundary -Content-Type: text/html; charset=utf-8 - -$email_html - ---nfcoremimeboundary -Content-Type: image/png;name="myorg-myfirstpipeline_logo.png" -Content-Transfer-Encoding: base64 -Content-ID: -Content-Disposition: inline; filename="myorg-myfirstpipeline_logo_light.png" - -<% out << new File("$projectDir/assets/myorg-myfirstpipeline_logo_light.png"). - bytes. - encodeBase64(). - toString(). - tokenize( '\n' )*. - toList()*. - collate( 76 )*. - collect { it.join() }. - flatten(). - join( '\n' ) %> - -<% -if (mqcFile){ -def mqcFileObj = new File("$mqcFile") -if (mqcFileObj.length() < mqcMaxSize){ -out << """ ---nfcoremimeboundary -Content-Type: text/html; name=\"multiqc_report\" -Content-Transfer-Encoding: base64 -Content-ID: -Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\" - -${mqcFileObj. - bytes. - encodeBase64(). - toString(). - tokenize( '\n' )*. - toList()*. - collate( 76 )*. - collect { it.join() }. - flatten(). - join( '\n' )} -""" -}} -%> - ---nfcoremimeboundary-- diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/base.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/base.config deleted file mode 100644 index 34cad808f..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/base.config +++ /dev/null @@ -1,62 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - myorg/myfirstpipeline Nextflow base config file -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - A 'blank slate' config file, appropriate for general use on most high performance - compute environments. Assumes that all software is installed and available on - the PATH. Runs in `local` mode - all jobs will be run on the logged in environment. ----------------------------------------------------------------------------------------- -*/ - -process { - - // TODO nf-core: Check the defaults for all processes - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } - - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' - - // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. - // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. - // If possible, it would be nice to keep the same label naming convention when - // adding in your local modules too. - // TODO nf-core: Customise requirements for specific processes. - // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors - withLabel:process_single { - cpus = { 1 } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } - } - withLabel:process_low { - cpus = { 2 * task.attempt } - memory = { 12.GB * task.attempt } - time = { 4.h * task.attempt } - } - withLabel:process_medium { - cpus = { 6 * task.attempt } - memory = { 36.GB * task.attempt } - time = { 8.h * task.attempt } - } - withLabel:process_high { - cpus = { 12 * task.attempt } - memory = { 72.GB * task.attempt } - time = { 16.h * task.attempt } - } - withLabel:process_long { - time = { 20.h * task.attempt } - } - withLabel:process_high_memory { - memory = { 200.GB * task.attempt } - } - withLabel:error_ignore { - errorStrategy = 'ignore' - } - withLabel:error_retry { - errorStrategy = 'retry' - maxRetries = 2 - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/modules.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/modules.config deleted file mode 100644 index 1da0fcec6..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/modules.config +++ /dev/null @@ -1,33 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. ----------------------------------------------------------------------------------------- -*/ - -process { - - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - - withName: 'SEQTK_TRIM' { - ext.args = "-b 5" - } - withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } - publishDir = [ - path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/test.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/test.config deleted file mode 100644 index 474ef3196..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/test.config +++ /dev/null @@ -1,31 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run myorg/myfirstpipeline -profile test, --outdir - ----------------------------------------------------------------------------------------- -*/ - -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '1.h' - ] -} - -params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' - - // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/test_full.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/test_full.config deleted file mode 100644 index 9b520728a..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/conf/test_full.config +++ /dev/null @@ -1,24 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running full-size tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a full size pipeline test. - - Use as follows: - nextflow run myorg/myfirstpipeline -profile test_full, --outdir - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'Full test profile' - config_profile_description = 'Full test dataset to check pipeline function' - - // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' - - // Fasta references - fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz' -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/README.md b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/README.md deleted file mode 100644 index 18062fa6b..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# myorg/myfirstpipeline: Documentation - -The myorg/myfirstpipeline documentation is split into the following pages: - -- [Usage](usage.md) - - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. -- [Output](output.md) - - An overview of the different results produced by the pipeline and how to interpret them. diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/output.md b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/output.md deleted file mode 100644 index 593ee5685..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/output.md +++ /dev/null @@ -1,47 +0,0 @@ -# myorg/myfirstpipeline: Output - -## Introduction - -This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. - -The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. - - - -## Pipeline overview - -The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: - -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline -- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution - -### MultiQC - -
-Output files - -- `multiqc/` - - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - - `multiqc_plots/`: directory containing static images from the report in various formats. - -
- -[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. - -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . - -### Pipeline information - -
-Output files - -- `pipeline_info/` - - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - - Parameters used by the pipeline run: `params.json`. - -
- -[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/usage.md b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/usage.md deleted file mode 100644 index 40429377b..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/docs/usage.md +++ /dev/null @@ -1,216 +0,0 @@ -# myorg/myfirstpipeline: Usage - -> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ - -## Introduction - - - -## Samplesheet input - -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. - -```bash ---input '[path to samplesheet file]' -``` - -### Multiple runs of the same sample - -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: - -```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz -``` - -### Full samplesheet - -The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. - -A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. - -```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, -``` - -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | - -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. - -## Running the pipeline - -The typical command for running the pipeline is as follows: - -```bash -nextflow run myorg/myfirstpipeline --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker -``` - -This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. - -Note that the pipeline will create the following files in your working directory: - -```bash -work # Directory containing the nextflow working files - # Finished results in specified location (defined with --outdir) -.nextflow_log # Log file from Nextflow -# Other nextflow hidden files, eg. history of pipeline runs and old logs. -``` - -If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. - -Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. - -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: - -The above pipeline run specified with a params file in yaml format: - -```bash -nextflow run myorg/myfirstpipeline -profile docker -params-file params.yaml -``` - -with: - -```yaml title="params.yaml" -input: './samplesheet.csv' -outdir: './results/' -genome: 'GRCh37' -<...> -``` - -You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). - -### Updating the pipeline - -When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: - -```bash -nextflow pull myorg/myfirstpipeline -``` - -### Reproducibility - -It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. - -First, go to the [myorg/myfirstpipeline releases page](https://github.com/myorg/myfirstpipeline/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. - -This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. - -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. - -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: - -## Core Nextflow arguments - -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: - -### `-profile` - -Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. - -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. - -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: - -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). - -Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! -They are loaded in sequence, so later profiles can overwrite earlier profiles. - -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. - -- `test` - - A profile with a complete configuration for automated testing - - Includes links to test data so needs no other parameters -- `docker` - - A generic configuration profile to be used with [Docker](https://docker.com/) -- `singularity` - - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) -- `podman` - - A generic configuration profile to be used with [Podman](https://podman.io/) -- `shifter` - - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) -- `charliecloud` - - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) -- `apptainer` - - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) -- `wave` - - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). -- `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. - -### `-resume` - -Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html). - -You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names. - -### `-c` - -Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information. - -## Custom configuration - -### Resource requests - -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. - -To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. - -### Custom Containers - -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. - -To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. - -### Custom Tool Arguments - -A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. - -To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. - -### nf-core/configs - -In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. - -See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files. - -If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). - -## Running in the background - -Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. - -The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file. - -Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time. -Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs). - -## Nextflow memory requirements - -In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. -We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`): - -```bash -NXF_OPTS='-Xms1g -Xmx4g' -``` diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/main.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/main.nf deleted file mode 100644 index de383a8bd..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/main.nf +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env nextflow -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - myorg/myfirstpipeline -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/myorg/myfirstpipeline ----------------------------------------------------------------------------------------- -*/ - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -include { MYFIRSTPIPELINE } from './workflows/myfirstpipeline' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_myfirstpipeline_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_myfirstpipeline_pipeline' -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOWS FOR PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// WORKFLOW: Run main analysis pipeline depending on type of input -// -workflow MYORG_MYFIRSTPIPELINE { - - take: - samplesheet // channel: samplesheet read in from --input - - main: - - // - // WORKFLOW: Run pipeline - // - MYFIRSTPIPELINE ( - samplesheet - ) - emit: - multiqc_report = MYFIRSTPIPELINE.out.multiqc_report // channel: /path/to/multiqc_report.html -} -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN MAIN WORKFLOW -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow { - - main: - // - // SUBWORKFLOW: Run initialisation tasks - // - PIPELINE_INITIALISATION ( - params.version, - params.validate_params, - params.monochrome_logs, - args, - params.outdir, - params.input - ) - - // - // WORKFLOW: Run main workflow - // - MYORG_MYFIRSTPIPELINE ( - PIPELINE_INITIALISATION.out.samplesheet - ) - // - // SUBWORKFLOW: Run completion tasks - // - PIPELINE_COMPLETION ( - params.email, - params.email_on_fail, - params.plaintext_email, - params.outdir, - params.monochrome_logs, - - MYORG_MYFIRSTPIPELINE.out.multiqc_report - ) -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules.json b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules.json deleted file mode 100644 index e37067859..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "name": "myorg/myfirstpipeline", - "homePage": "https://github.com/myorg/myfirstpipeline", - "repos": { - "https://github.com/nf-core/modules.git": { - "modules": { - "nf-core": { - "multiqc": { - "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": ["modules"] - }, - "seqtk/trim": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - } - } - }, - "subworkflows": { - "nf-core": { - "utils_nextflow_pipeline": { - "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": ["subworkflows"] - }, - "utils_nfcore_pipeline": { - "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": ["subworkflows"] - }, - "utils_nfschema_plugin": { - "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": ["subworkflows"] - } - } - } - } - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/local/fastqe.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/local/fastqe.nf deleted file mode 100644 index 827843d98..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/local/fastqe.nf +++ /dev/null @@ -1,35 +0,0 @@ -process FASTQE { - tag "$meta.id" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqe:0.3.3--pyhdfd78af_0': - 'biocontainers/fastqe:0.3.3--pyhdfd78af_0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.tsv"), emit: tsv - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '0.3.3' - """ - fastqe \\ - $args \\ - $reads \\ - --output ${prefix}.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqe: $VERSION - END_VERSIONS - """ -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/environment.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/environment.yml deleted file mode 100644 index 6f5b867b7..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::multiqc=1.25.1 diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/main.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/main.nf deleted file mode 100644 index cc0643e1d..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/main.nf +++ /dev/null @@ -1,63 +0,0 @@ -process MULTIQC { - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" - - input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - path(replace_names) - path(sample_names) - - output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' - def replace = replace_names ? "--replace-names ${replace_names}" : '' - def samples = sample_names ? "--sample-names ${sample_names}" : '' - """ - multiqc \\ - --force \\ - $args \\ - $config \\ - $prefix \\ - $extra_config \\ - $logo \\ - $replace \\ - $samples \\ - . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ - - stub: - """ - mkdir multiqc_data - mkdir multiqc_plots - touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/meta.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/meta.yml deleted file mode 100644 index b16c18792..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/meta.yml +++ /dev/null @@ -1,78 +0,0 @@ -name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into - a single report -keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report -tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] - identifier: biotools:multiqc -input: - - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" -output: - - report: - - "*multiqc_report.html": - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - - "*_plots": - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" -maintainers: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/main.nf.test b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/main.nf.test deleted file mode 100644 index 33316a7dd..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/main.nf.test +++ /dev/null @@ -1,92 +0,0 @@ -nextflow_process { - - name "Test Process MULTIQC" - script "../main.nf" - process "MULTIQC" - - tag "modules" - tag "modules_nfcore" - tag "multiqc" - - config "./nextflow.config" - - test("sarscov2 single-end [fastqc]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) - } - - } - - test("sarscov2 single-end [fastqc] [config]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) - } - } - - test("sarscov2 single-end [fastqc] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } - ) - } - - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/main.nf.test.snap b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/main.nf.test.snap deleted file mode 100644 index 261dc0fac..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/main.nf.test.snap +++ /dev/null @@ -1,41 +0,0 @@ -{ - "multiqc_versions_single": { - "content": [ - [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-02T17:51:46.317523" - }, - "multiqc_stub": { - "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-02T17:52:20.680978" - }, - "multiqc_versions_config": { - "content": [ - [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-02T17:52:09.185842" - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/nextflow.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/nextflow.config deleted file mode 100644 index c537a6a3e..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'MULTIQC' { - ext.prefix = null - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/tags.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d37..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/environment.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/environment.yml deleted file mode 100644 index 693aa5c17..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::seqtk=1.4 diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/main.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/main.nf deleted file mode 100644 index 0f7e4d7f8..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/main.nf +++ /dev/null @@ -1,38 +0,0 @@ -process SEQTK_TRIM { - tag "$meta.id" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_1' : - 'biocontainers/seqtk:1.4--he4a0461_1' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.fastq.gz"), emit: reads - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - printf "%s\\n" $reads | while read f; - do - seqtk \\ - trimfq \\ - $args \\ - \$f \\ - | gzip --no-name > ${prefix}_\$(basename \$f) - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS - """ -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/meta.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/meta.yml deleted file mode 100644 index 3a0198ac0..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/meta.yml +++ /dev/null @@ -1,45 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: seqtk_trim -description: Trim low quality bases from FastQ files -keywords: - - trimfq - - fastq - - seqtk -tools: - - "seqtk": - description: "Seqtk is a fast and lightweight tool for processing sequences in - the FASTA or FASTQ format" - homepage: https://github.com/lh3/seqtk - documentation: https://docs.csc.fi/apps/seqtk/ - tool_dev_url: https://github.com/lh3/seqtk - licence: ["MIT"] - identifier: biotools:seqtk - -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files - pattern: "*.{fastq.gz}" -output: - - reads: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.fastq.gz": - type: file - description: Filtered FastQ files - pattern: "*.{fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@laramiellindsey" diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/main.nf.test b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/main.nf.test deleted file mode 100644 index be53186d8..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/main.nf.test +++ /dev/null @@ -1,65 +0,0 @@ -nextflow_process { - - name "Test Process SEQTK_TRIM" - script "modules/nf-core/seqtk/trim/main.nf" - process "SEQTK_TRIM" - - tag "modules" - tag "modules_nfcore" - tag "seqtk" - tag "seqtk/trim" - - test("Single-end") { - - when { - params { - outdir = $outputDir - } - process { - """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ] - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match()} - ) - } - - } - -test("Paired-end") { - - when { - params { - outdir = $outputDir - } - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) - ] - ] - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match()} - ) - } - - } - -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/main.nf.test.snap b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/main.nf.test.snap deleted file mode 100644 index 90da25d2b..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/main.nf.test.snap +++ /dev/null @@ -1,78 +0,0 @@ -{ - "Single-end": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" - ] - ], - "1": [ - "versions.yml:md5,d061ca0231d089b087e22d2001cd7c32" - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" - ] - ], - "versions": [ - "versions.yml:md5,d061ca0231d089b087e22d2001cd7c32" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-03T06:10:55.544977" - }, - "Paired-end": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec", - "test_test_2.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42" - ] - ] - ], - "1": [ - "versions.yml:md5,d061ca0231d089b087e22d2001cd7c32" - ], - "reads": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec", - "test_test_2.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42" - ] - ] - ], - "versions": [ - "versions.yml:md5,d061ca0231d089b087e22d2001cd7c32" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-03T06:11:38.487227" - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/tags.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/tags.yml deleted file mode 100644 index 250a1382f..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/modules/nf-core/seqtk/trim/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -seqtk/trim: - - "modules/nf-core/seqtk/trim/**" diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/nextflow.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/nextflow.config deleted file mode 100644 index e94053c29..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/nextflow.config +++ /dev/null @@ -1,242 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - myorg/myfirstpipeline Nextflow config file -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Default config options for all compute environments ----------------------------------------------------------------------------------------- -*/ - -// Global default params, used in configs -params { - - // TODO nf-core: Specify your pipeline's command line flags - // Input options - input = null - - skip_trim = false - - // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - - - // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - - help = false - help_full = false - show_hidden = false - version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - - // Config options - config_profile_name = null - config_profile_description = null - - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_contact = null - config_profile_url = null - - // Schema validation default options - validate_params = true -} - -// Load base.config by default for all pipelines -includeConfig 'conf/base.config' - -profiles { - debug { - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - cleanup = false - nextflow.enable.configProcessNamesValidation = true - } - conda { - conda.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda'] - apptainer.enabled = false - } - mamba { - conda.enabled = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - } - docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' - } - arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' - } - singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - } - podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - } - shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - } - charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false - } - apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - } - wave { - apptainer.ociAutoPull = true - singularity.ociAutoPull = true - wave.enabled = true - wave.freeze = true - wave.strategy = 'conda,container' - } - - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } -} - -// Load nf-core custom profiles from different Institutions -includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" - -// Load myorg/myfirstpipeline custom profiles from different institutions. -// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/myfirstpipeline.config" : "/dev/null" - -// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' -charliecloud.registry = 'quay.io' - - - -// Export these variables to prevent local Python/R libraries from conflicting with those in the container -// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. -// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. - -env { - PYTHONNOUSERSITE = 1 - R_PROFILE_USER = "/.Rprofile" - R_ENVIRON_USER = "/.Renviron" - JULIA_DEPOT_PATH = "/usr/local/share/julia" -} - -// Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" - -// Disable process selector warnings by default. Use debug profile to enable warnings. -nextflow.enable.configProcessNamesValidation = false - -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') -timeline { - enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" -} -report { - enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" -} -trace { - enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" -} -dag { - enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" -} - -manifest { - name = 'myorg/myfirstpipeline' - author = """gitpod""" - homePage = 'https://github.com/myorg/myfirstpipeline' - description = """My first pipeline""" - mainScript = 'main.nf' - nextflowVersion = '!>=24.04.2' - version = '1.0.0dev' - doi = '' -} - -// Nextflow plugins -plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} - -validation { - defaultIgnoreParams = ["genomes"] - help { - enabled = true - command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " - fullParameter = "help_full" - showHiddenParameter = "show_hidden" - - } -} - -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/nextflow_schema.json b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/nextflow_schema.json deleted file mode 100644 index 327a92417..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/nextflow_schema.json +++ /dev/null @@ -1,188 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/myorg/myfirstpipeline/master/nextflow_schema.json", - "title": "myorg/myfirstpipeline pipeline parameters", - "description": "My first pipeline", - "type": "object", - "$defs": { - "input_output_options": { - "title": "Input/output options", - "type": "object", - "fa_icon": "fas fa-terminal", - "description": "Define where the pipeline should find input data and save output data.", - "required": ["input", "outdir"], - "properties": { - "input": { - "type": "string", - "format": "file-path", - "exists": true, - "schema": "assets/schema_input.json", - "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", - "description": "Path to comma-separated file containing information about the samples in the experiment.", - "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.", - "fa_icon": "fas fa-file-csv" - }, - "outdir": { - "type": "string", - "format": "directory-path", - "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", - "fa_icon": "fas fa-folder-open" - }, - "skip_trim": { - "type": "boolean" - }, - "email": { - "type": "string", - "description": "Email address for completion summary.", - "fa_icon": "fas fa-envelope", - "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", - "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" - }, - "multiqc_title": { - "type": "string", - "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", - "fa_icon": "fas fa-file-signature" - } - } - }, - "institutional_config_options": { - "title": "Institutional config options", - "type": "object", - "fa_icon": "fas fa-university", - "description": "Parameters used to describe centralised config profiles. These should not be edited.", - "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", - "properties": { - "custom_config_version": { - "type": "string", - "description": "Git commit id for Institutional configs.", - "default": "master", - "hidden": true, - "fa_icon": "fas fa-users-cog" - }, - "custom_config_base": { - "type": "string", - "description": "Base directory for Institutional configs.", - "default": "https://raw.githubusercontent.com/nf-core/configs/master", - "hidden": true, - "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", - "fa_icon": "fas fa-users-cog" - }, - "config_profile_name": { - "type": "string", - "description": "Institutional config name.", - "hidden": true, - "fa_icon": "fas fa-users-cog" - }, - "config_profile_description": { - "type": "string", - "description": "Institutional config description.", - "hidden": true, - "fa_icon": "fas fa-users-cog" - }, - "config_profile_contact": { - "type": "string", - "description": "Institutional config contact information.", - "hidden": true, - "fa_icon": "fas fa-users-cog" - }, - "config_profile_url": { - "type": "string", - "description": "Institutional config URL link.", - "hidden": true, - "fa_icon": "fas fa-users-cog" - } - } - }, - "generic_options": { - "title": "Generic options", - "type": "object", - "fa_icon": "fas fa-file-import", - "description": "Less common options for the pipeline, typically set in a config file.", - "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", - "properties": { - "version": { - "type": "boolean", - "description": "Display version and exit.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, - "publish_dir_mode": { - "type": "string", - "default": "copy", - "description": "Method used to save pipeline results to output directory.", - "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", - "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], - "hidden": true - }, - "email_on_fail": { - "type": "string", - "description": "Email address for completion summary, only when pipeline fails.", - "fa_icon": "fas fa-exclamation-triangle", - "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$", - "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.", - "hidden": true - }, - "plaintext_email": { - "type": "boolean", - "description": "Send plain-text email instead of HTML.", - "fa_icon": "fas fa-remove-format", - "hidden": true - }, - "max_multiqc_email_size": { - "type": "string", - "description": "File size limit when attaching MultiQC reports to summary emails.", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "default": "25.MB", - "fa_icon": "fas fa-file-upload", - "hidden": true - }, - "monochrome_logs": { - "type": "boolean", - "description": "Do not use coloured log outputs.", - "fa_icon": "fas fa-palette", - "hidden": true - }, - "multiqc_config": { - "type": "string", - "format": "file-path", - "description": "Custom config file to supply to MultiQC.", - "fa_icon": "fas fa-cog", - "hidden": true - }, - "multiqc_logo": { - "type": "string", - "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", - "fa_icon": "fas fa-image", - "hidden": true - }, - "validate_params": { - "type": "boolean", - "description": "Boolean whether to validate parameters against the schema at runtime", - "default": true, - "fa_icon": "fas fa-check-square", - "hidden": true - }, - "pipelines_testdata_base_path": { - "type": "string", - "fa_icon": "far fa-check-circle", - "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", - "hidden": true - } - } - } - }, - "allOf": [ - { - "$ref": "#/$defs/input_output_options" - }, - { - "$ref": "#/$defs/institutional_config_options" - }, - { - "$ref": "#/$defs/generic_options" - } - ] -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/local/utils_nfcore_myfirstpipeline_pipeline/main.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/local/utils_nfcore_myfirstpipeline_pipeline/main.nf deleted file mode 100644 index 4e4a4ece4..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/local/utils_nfcore_myfirstpipeline_pipeline/main.nf +++ /dev/null @@ -1,222 +0,0 @@ -// -// Subworkflow with functionality specific to the myorg/myfirstpipeline pipeline -// - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' -include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' -include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - SUBWORKFLOW TO INITIALISE PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow PIPELINE_INITIALISATION { - - take: - version // boolean: Display version and exit - validate_params // boolean: Boolean whether to validate parameters against the schema at runtime - monochrome_logs // boolean: Do not use coloured log outputs - nextflow_cli_args // array: List of positional nextflow CLI args - outdir // string: The output directory where the results will be saved - input // string: Path to input samplesheet - - main: - - ch_versions = Channel.empty() - - // - // Print version and exit if required and dump pipeline parameters to JSON file - // - UTILS_NEXTFLOW_PIPELINE ( - version, - true, - outdir, - workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 - ) - - // - // Validate parameters and generate parameter summary to stdout - // - UTILS_NFSCHEMA_PLUGIN ( - workflow, - validate_params, - null - ) - - // - // Check config provided to the pipeline - // - UTILS_NFCORE_PIPELINE ( - nextflow_cli_args - ) - - // - // Create channel from input file provided through params.input - // - - Channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { samplesheet -> - validateInputSamplesheet(samplesheet) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } - - emit: - samplesheet = ch_samplesheet - versions = ch_versions -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - SUBWORKFLOW FOR PIPELINE COMPLETION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow PIPELINE_COMPLETION { - - take: - email // string: email address - email_on_fail // string: email address sent on pipeline failure - plaintext_email // boolean: Send plain-text email instead of HTML - outdir // path: Path to output directory where results will be published - monochrome_logs // boolean: Disable ANSI colour codes in log output - - multiqc_report // string: Path to MultiQC report - - main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - - // - // Completion email and summary - // - workflow.onComplete { - if (email || email_on_fail) { - completionEmail( - summary_params, - email, - email_on_fail, - plaintext_email, - outdir, - monochrome_logs, - multiqc_report.toList() - ) - } - - completionSummary(monochrome_logs) - } - - workflow.onError { - log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" - } -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// Validate channels from input samplesheet -// -def validateInputSamplesheet(input) { - def (metas, fastqs) = input[1..2] - - // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 - if (!endedness_ok) { - error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") - } - - return [ metas[0], fastqs ] -} -// -// Generate methods description for MultiQC -// -def toolCitationText() { - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text -} - -def toolBibliographyText() { - // TODO nf-core: Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " - ].join(' ').trim() - - return reference_text -} - -def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = workflow.toMap() - meta["manifest_map"] = workflow.manifest.toMap() - - // Pipeline DOI - if (meta.manifest_map.doi) { - // Using a loop to handle multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - def temp_doi_ref = "" - def manifest_doi = meta.manifest_map.doi.tokenize(",") - manifest_doi.each { doi_ref -> - temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " - } - meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) - } else meta["doi_text"] = "" - meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - // meta["tool_bibliography"] = toolBibliographyText() - - - def methods_text = mqc_methods_yaml.text - - def engine = new groovy.text.SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html.toString() -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/main.nf deleted file mode 100644 index 0fcbf7b3f..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ /dev/null @@ -1,124 +0,0 @@ -// -// Subworkflow with functionality that may be useful for any Nextflow pipeline -// - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow UTILS_NEXTFLOW_PIPELINE { - take: - print_version // boolean: print version - dump_parameters // boolean: dump parameters - outdir // path: base directory used to publish pipeline results - check_conda_channels // boolean: check conda channels - - main: - - // - // Print workflow version and exit on --version - // - if (print_version) { - log.info("${workflow.manifest.name} ${getWorkflowVersion()}") - System.exit(0) - } - - // - // Dump pipeline parameters to a JSON file - // - if (dump_parameters && outdir) { - dumpParametersToJSON(outdir) - } - - // - // When running with Conda, warn if channels have not been set-up appropriately - // - if (check_conda_channels) { - checkCondaChannels() - } - - emit: - dummy_emit = true -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// Generate version string -// -def getWorkflowVersion() { - def version_string = "" as String - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string -} - -// -// Dump pipeline parameters to a JSON file -// -def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) - temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - - nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() -} - -// -// When running with -profile conda, warn if channels have not been set-up appropriately -// -def checkCondaChannels() { - def parser = new org.yaml.snakeyaml.Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } - catch (NullPointerException e) { - log.warn("Could not verify conda channel configuration.") - return null - } - catch (IOException e) { - log.warn("Could not verify conda channel configuration.") - return null - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } - - if (channels_missing | channel_priority_violation) { - log.warn """\ - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - There is a problem with your Conda configuration! - You will need to set-up the conda-forge and bioconda channels correctly. - Please refer to https://bioconda.github.io/ - The observed channel order is - ${channels} - but the following channel order is required: - ${required_channels_in_order} - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - """.stripIndent(true) - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml deleted file mode 100644 index e5c3a0a82..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml +++ /dev/null @@ -1,38 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NEXTFLOW_PIPELINE" -description: Subworkflow with functionality that may be useful for any Nextflow pipeline -keywords: - - utility - - pipeline - - initialise - - version -components: [] -input: - - print_version: - type: boolean - description: | - Print the version of the pipeline and exit - - dump_parameters: - type: boolean - description: | - Dump the parameters of the pipeline to a JSON file - - output_directory: - type: directory - description: Path to output dir to write JSON file to. - pattern: "results/" - - check_conda_channel: - type: boolean - description: | - Check if the conda channel priority is correct. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" - - "@drpatelh" -maintainers: - - "@adamrtalbot" - - "@drpatelh" - - "@maxulysse" diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test deleted file mode 100644 index 68718e4f5..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ /dev/null @@ -1,54 +0,0 @@ - -nextflow_function { - - name "Test Functions" - script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" - config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" - tag 'subworkflows' - tag 'utils_nextflow_pipeline' - tag 'subworkflows/utils_nextflow_pipeline' - - test("Test Function getWorkflowVersion") { - - function "getWorkflowVersion" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function dumpParametersToJSON") { - - function "dumpParametersToJSON" - - when { - function { - """ - // define inputs of the function here. Example: - input[0] = "$outputDir" - """.stripIndent() - } - } - - then { - assertAll( - { assert function.success } - ) - } - } - - test("Test Function checkCondaChannels") { - - function "checkCondaChannels" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap deleted file mode 100644 index 846287c41..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ /dev/null @@ -1,20 +0,0 @@ -{ - "Test Function getWorkflowVersion": { - "content": [ - "v9.9.9" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:02:05.308243" - }, - "Test Function checkCondaChannels": { - "content": null, - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:02:12.425833" - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test deleted file mode 100644 index ca964ce8e..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ /dev/null @@ -1,111 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NEXTFLOW_PIPELINE" - script "../main.nf" - config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" - workflow "UTILS_NEXTFLOW_PIPELINE" - tag 'subworkflows' - tag 'utils_nextflow_pipeline' - tag 'subworkflows/utils_nextflow_pipeline' - - test("Should run no inputs") { - - when { - workflow { - """ - print_version = false - dump_parameters = false - outdir = null - check_conda_channels = false - - input[0] = print_version - input[1] = dump_parameters - input[2] = outdir - input[3] = check_conda_channels - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should print version") { - - when { - workflow { - """ - print_version = true - dump_parameters = false - outdir = null - check_conda_channels = false - - input[0] = print_version - input[1] = dump_parameters - input[2] = outdir - input[3] = check_conda_channels - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) - } - } - - test("Should dump params") { - - when { - workflow { - """ - print_version = false - dump_parameters = true - outdir = 'results' - check_conda_channels = false - - input[0] = false - input[1] = true - input[2] = outdir - input[3] = false - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should not create params JSON if no output directory") { - - when { - workflow { - """ - print_version = false - dump_parameters = true - outdir = null - check_conda_channels = false - - input[0] = false - input[1] = true - input[2] = outdir - input[3] = false - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config deleted file mode 100644 index a09572e5b..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -manifest { - name = 'nextflow_workflow' - author = """nf-core""" - homePage = 'https://127.0.0.1' - description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' - version = '9.9.9' - doi = 'https://doi.org/10.5281/zenodo.5070524' -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f84761125..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/main.nf deleted file mode 100644 index 5cb7bafef..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ /dev/null @@ -1,462 +0,0 @@ -// -// Subworkflow with utility functions specific to the nf-core pipeline template -// - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow UTILS_NFCORE_PIPELINE { - take: - nextflow_cli_args - - main: - valid_config = checkConfigProvided() - checkProfileProvided(nextflow_cli_args) - - emit: - valid_config -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// Warn if a -profile or Nextflow config has not been provided to run the pipeline -// -def checkConfigProvided() { - def valid_config = true as Boolean - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn( - "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " - ) - valid_config = false - } - return valid_config -} - -// -// Exit pipeline if --profile contains spaces -// -def checkProfileProvided(nextflow_cli_args) { - if (workflow.profile.endsWith(',')) { - error( - "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" - ) - } - if (nextflow_cli_args[0]) { - log.warn( - "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" - ) - } -} - -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - def manifest_doi = workflow.manifest.doi.tokenize(",") - // Handling multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - manifest_doi.each { doi_ref -> - temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - -// -// Generate workflow version string -// -def getWorkflowVersion() { - def version_string = "" as String - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string -} - -// -// Get software versions for pipeline -// -def processVersionsFromYAML(yaml_file) { - def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } - return yaml.dumpAsMap(versions).trim() -} - -// -// Get workflow version for pipeline -// -def workflowVersionToYAML() { - return """ - Workflow: - ${workflow.manifest.name}: ${getWorkflowVersion()} - Nextflow: ${workflow.nextflow.version} - """.stripIndent().trim() -} - -// -// Get channel of software versions used in pipeline in YAML format -// -def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) -} - -// -// Get workflow summary for MultiQC -// -def paramsSummaryMultiqc(summary_params) { - def summary_section = '' - summary_params - .keySet() - .each { group -> - def group_params = summary_params.get(group) - // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    ${group}

    \n" - summary_section += "
    \n" - group_params - .keySet() - .sort() - .each { param -> - summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" - } - summary_section += "
    \n" - } - } - - def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - - return yaml_file_text -} - -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - -// -// ANSII colours used for terminal logging -// -def logColours(monochrome_logs=true) { - def colorcodes = [:] as Map - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes -} - -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") - } - mqc_report = mqc_report[0] - } - } - } - catch (Exception all) { - if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") - } - } - return mqc_report -} - -// -// Construct and send completion email -// -def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { - - // Set up the e-mail variables - def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" - if (!workflow.success) { - subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" - } - - def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) { - misc_fields['Pipeline repository Git URL'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['Pipeline repository Git Commit'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['Pipeline Git branch/tag'] = workflow.revision - } - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = getWorkflowVersion() - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) - - // Check if we are only sending emails on failure - def email_address = email - if (!email && email_on_fail && !workflow.success) { - email_address = email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("${workflow.projectDir}/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("${workflow.projectDir}/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] - def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - def colors = logColours(monochrome_logs) as Map - if (email_address) { - try { - if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - ['sendmail', '-t'].execute() << sendmail_html - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") - } - catch (Exception all) { - // Catch failures and try with plaintext - def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] - mail_cmd.execute() << email_html - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") - output_tf.delete() -} - -// -// Print pipeline summary on completion -// -def completionSummary(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") - } - else { - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") - } - } - else { - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") - } -} - -// -// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack -// -def imNotification(summary_params, hook_url) { - def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) { - misc_fields['repository'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['commitid'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['revision'] = workflow.revision - } - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = getWorkflowVersion() - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("${workflow.projectDir}/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection() - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")) - def postRC = post.getResponseCode() - if (!postRC.equals(200)) { - log.warn(post.getErrorStream().getText()) - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml deleted file mode 100644 index d08d24342..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml +++ /dev/null @@ -1,24 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFCORE_PIPELINE" -description: Subworkflow with utility functions specific to the nf-core pipeline template -keywords: - - utility - - pipeline - - initialise - - version -components: [] -input: - - nextflow_cli_args: - type: list - description: | - Nextflow CLI positional arguments -output: - - success: - type: boolean - description: | - Dummy output to indicate success -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test deleted file mode 100644 index 1dc317f8f..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ /dev/null @@ -1,134 +0,0 @@ - -nextflow_function { - - name "Test Functions" - script "../main.nf" - config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "utils_nfcore_pipeline" - tag "subworkflows/utils_nfcore_pipeline" - - test("Test Function checkConfigProvided") { - - function "checkConfigProvided" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function checkProfileProvided") { - - function "checkProfileProvided" - - when { - function { - """ - input[0] = [] - """ - } - } - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { - - function "nfCoreLogo" - - when { - function { - """ - input[0] = false - """ - } - } - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function dashedLine") { - - function "dashedLine" - - when { - function { - """ - input[0] = false - """ - } - } - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function without logColours") { - - function "logColours" - - when { - function { - """ - input[0] = true - """ - } - } - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function with logColours") { - function "logColours" - - when { - function { - """ - input[0] = false - """ - } - } - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap deleted file mode 100644 index facbdcfdc..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ /dev/null @@ -1,166 +0,0 @@ -{ - "Test Function checkProfileProvided": { - "content": null, - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:03.360873" - }, - "Test Function checkConfigProvided": { - "content": [ - true - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:02:59.729647" - }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, - "Test Function without logColours": { - "content": [ - { - "reset": "", - "bold": "", - "dim": "", - "underlined": "", - "blink": "", - "reverse": "", - "hidden": "", - "black": "", - "red": "", - "green": "", - "yellow": "", - "blue": "", - "purple": "", - "cyan": "", - "white": "", - "bblack": "", - "bred": "", - "bgreen": "", - "byellow": "", - "bblue": "", - "bpurple": "", - "bcyan": "", - "bwhite": "", - "ublack": "", - "ured": "", - "ugreen": "", - "uyellow": "", - "ublue": "", - "upurple": "", - "ucyan": "", - "uwhite": "", - "iblack": "", - "ired": "", - "igreen": "", - "iyellow": "", - "iblue": "", - "ipurple": "", - "icyan": "", - "iwhite": "", - "biblack": "", - "bired": "", - "bigreen": "", - "biyellow": "", - "biblue": "", - "bipurple": "", - "bicyan": "", - "biwhite": "" - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:17.969323" - }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, - "Test Function with logColours": { - "content": [ - { - "reset": "\u001b[0m", - "bold": "\u001b[1m", - "dim": "\u001b[2m", - "underlined": "\u001b[4m", - "blink": "\u001b[5m", - "reverse": "\u001b[7m", - "hidden": "\u001b[8m", - "black": "\u001b[0;30m", - "red": "\u001b[0;31m", - "green": "\u001b[0;32m", - "yellow": "\u001b[0;33m", - "blue": "\u001b[0;34m", - "purple": "\u001b[0;35m", - "cyan": "\u001b[0;36m", - 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} -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test deleted file mode 100644 index 8940d32d1..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test +++ /dev/null @@ -1,29 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFCORE_PIPELINE" - script "../main.nf" - config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" - workflow "UTILS_NFCORE_PIPELINE" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "utils_nfcore_pipeline" - tag "subworkflows/utils_nfcore_pipeline" - - test("Should run without failures") { - - when { - workflow { - """ - input[0] = [] - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap deleted file mode 100644 index 84ee1e1d1..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ /dev/null @@ -1,19 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - true - ], - "valid_config": [ - true - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:25.726491" - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config deleted file mode 100644 index d0a926bf6..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -manifest { - name = 'nextflow_workflow' - author = """nf-core""" - homePage = 'https://127.0.0.1' - description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' - version = '9.9.9' - doi = 'https://doi.org/10.5281/zenodo.5070524' -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c9a..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/main.nf deleted file mode 100644 index 93de2a524..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ /dev/null @@ -1,45 +0,0 @@ -// -// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary -// - -include { paramsSummaryLog } from 'plugin/nf-schema' -include { validateParameters } from 'plugin/nf-schema' - -workflow UTILS_NFSCHEMA_PLUGIN { - - take: - input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow - validate_params // boolean: validate the parameters - parameters_schema // string: path to the parameters JSON schema. - // this has to be the same as the schema given to `validation.parametersSchema` - // when this input is empty it will automatically use the configured schema or - // "${projectDir}/nextflow_schema.json" as default. This input should not be empty - // for meta pipelines - - main: - - // - // Print parameter summary to stdout. This will display the parameters - // that differ from the default given in the JSON schema - // - if(parameters_schema) { - log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) - } else { - log.info paramsSummaryLog(input_workflow) - } - - // - // Validate the parameters using nextflow_schema.json or the schema - // given via the validation.parametersSchema configuration option - // - if(validate_params) { - if(parameters_schema) { - validateParameters(parameters_schema:parameters_schema) - } else { - validateParameters() - } - } - - emit: - dummy_emit = true -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/meta.yml deleted file mode 100644 index f7d9f0288..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ /dev/null @@ -1,35 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "utils_nfschema_plugin" -description: Run nf-schema to validate parameters and create a summary of changed parameters -keywords: - - validation - - JSON schema - - plugin - - parameters - - summary -components: [] -input: - - input_workflow: - type: object - description: | - The workflow object of the used pipeline. - This object contains meta data used to create the params summary log - - validate_params: - type: boolean - description: Validate the parameters and error if invalid. - - parameters_schema: - type: string - description: | - Path to the parameters JSON schema. - This has to be the same as the schema given to the `validation.parametersSchema` config - option. When this input is empty it will automatically use the configured schema or - "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way - for meta pipelines. -output: - - dummy_emit: - type: boolean - description: Dummy emit to make nf-core subworkflows lint happy -authors: - - "@nvnieuwk" -maintainers: - - "@nvnieuwk" diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test deleted file mode 100644 index 842dc432a..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ /dev/null @@ -1,117 +0,0 @@ -nextflow_workflow { - - name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" - script "../main.nf" - workflow "UTILS_NFSCHEMA_PLUGIN" - - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/utils_nfschema_plugin" - tag "plugin/nf-schema" - - config "./nextflow.config" - - test("Should run nothing") { - - when { - - params { - test_data = '' - } - - workflow { - """ - validate_params = false - input[0] = workflow - input[1] = validate_params - input[2] = "" - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should validate params") { - - when { - - params { - test_data = '' - outdir = 1 - } - - workflow { - """ - validate_params = true - input[0] = workflow - input[1] = validate_params - input[2] = "" - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } - ) - } - } - - test("Should run nothing - custom schema") { - - when { - - params { - test_data = '' - } - - workflow { - """ - validate_params = false - input[0] = workflow - input[1] = validate_params - input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should validate params - custom schema") { - - when { - - params { - test_data = '' - outdir = 1 - } - - workflow { - """ - validate_params = true - input[0] = workflow - input[1] = validate_params - input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config deleted file mode 100644 index 478fb8a05..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -plugins { - id "nf-schema@2.1.0" -} - -validation { - parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - monochromeLogs = true -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json deleted file mode 100644 index 331e0d2f4..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", - "title": ". pipeline parameters", - "description": "", - "type": "object", - "$defs": { - "input_output_options": { - "title": "Input/output options", - "type": "object", - "fa_icon": "fas fa-terminal", - "description": "Define where the pipeline should find input data and save output data.", - "required": ["outdir"], - "properties": { - "validate_params": { - "type": "boolean", - "description": "Validate parameters?", - "default": true, - "hidden": true - }, - "outdir": { - "type": "string", - "format": "directory-path", - "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", - "fa_icon": "fas fa-folder-open" - }, - "test_data_base": { - "type": "string", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", - "description": "Base for test data directory", - "hidden": true - }, - "test_data": { - "type": "string", - "description": "Fake test data param", - "hidden": true - } - } - }, - "generic_options": { - "title": "Generic options", - "type": "object", - "fa_icon": "fas fa-file-import", - "description": "Less common options for the pipeline, typically set in a config file.", - "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", - "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, - "version": { - "type": "boolean", - "description": "Display version and exit.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, - "logo": { - "type": "boolean", - "default": true, - "description": "Display nf-core logo in console output.", - "fa_icon": "fas fa-image", - "hidden": true - }, - "singularity_pull_docker_container": { - "type": "boolean", - "description": "Pull Singularity container from Docker?", - "hidden": true - }, - "publish_dir_mode": { - "type": "string", - "default": "copy", - "description": "Method used to save pipeline results to output directory.", - "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", - "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], - "hidden": true - }, - "monochrome_logs": { - "type": "boolean", - "description": "Use monochrome_logs", - "hidden": true - } - } - } - }, - "allOf": [ - { - "$ref": "#/$defs/input_output_options" - }, - { - "$ref": "#/$defs/generic_options" - } - ] -} diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/tower.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/tower.yml deleted file mode 100644 index 787aedfe9..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/tower.yml +++ /dev/null @@ -1,5 +0,0 @@ -reports: - multiqc_report.html: - display: "MultiQC HTML report" - samplesheet.csv: - display: "Auto-created samplesheet with collated metadata and FASTQ paths" diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/workflows/myfirstpipeline.nf b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/workflows/myfirstpipeline.nf deleted file mode 100644 index 831740723..000000000 --- a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/workflows/myfirstpipeline.nf +++ /dev/null @@ -1,100 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ -include { FASTQE } from '../modules/local/fastqe' -include { SEQTK_TRIM } from '../modules/nf-core/seqtk/trim/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_myfirstpipeline_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN MAIN WORKFLOW -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow MYFIRSTPIPELINE { - - take: - ch_samplesheet // channel: samplesheet read in from --input - main: - - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() - ch_samplesheet.view() - - // - // MODULE: Run SEQTK_TRIM - // - if (!params.skip_trim) { - - ch_seqtk_in = ch_samplesheet.branch { meta, reads -> - to_trim: meta["sequencer"] == "sequencer2" - other: true - } - - SEQTK_TRIM ( - ch_seqtk_in.to_trim - ) - ch_trimmed = SEQTK_TRIM.out.reads - ch_versions = ch_versions.mix(SEQTK_TRIM.out.versions.first()) - } - - FASTQE(ch_samplesheet) - ch_versions = ch_versions.mix(FASTQE.out.versions.first()) - - // - // Collate and save software versions - // - softwareVersionsToYAML(ch_versions) - .collectFile( - storeDir: "${params.outdir}/pipeline_info", - name: '' + 'pipeline_software_' + 'mqc_' + 'versions.yml', - sort: true, - newLine: true - ).set { ch_collated_versions } - - - // - // MODULE: MultiQC - // - ch_multiqc_config = Channel.fromPath( - "$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() - - summary_params = paramsSummaryMap( - workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), - [], - [] - ) - - emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html - versions = ch_versions // channel: [ path(versions.yml) ] - -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ diff --git a/hello-nextflow/hello-nf-test/demo-params.json b/hello-nextflow/hello-nf-test/demo-params.json deleted file mode 100644 index 59be1e1d4..000000000 --- a/hello-nextflow/hello-nf-test/demo-params.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "reads_bam": "data/sample_bams.txt", - "outdir": "results_genomics", - "reference": "data/ref/ref.fasta", - "reference_index": "data/ref/ref.fasta.fai", - "reference_dict": "data/ref/ref.dict", - "intervals": "data/ref/intervals.bed", - "cohort_name": "family_trio" -} diff --git a/hello-nextflow/hello-nf-test/main.nf b/hello-nextflow/hello-nf-test/main.nf deleted file mode 100644 index 3e55a0d15..000000000 --- a/hello-nextflow/hello-nf-test/main.nf +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env nextflow - -// Include modules -include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf' -include { GATK_HAPLOTYPECALLER } from './modules/local/gatk/haplotypecaller/main.nf' -include { GATK_JOINTGENOTYPING } from './modules/local/gatk/jointgenotyping/main.nf' - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) - - // Collect variant calling outputs across samples - all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect() - all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect() - - // Combine GVCFs into a GenomicsDB data store and apply joint genotyping - GATK_JOINTGENOTYPING( - all_gvcfs_ch, - all_idxs_ch, - intervals_file, - params.cohort_name, - ref_file, - ref_index_file, - ref_dict_file - ) -} diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf b/hello-nextflow/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf deleted file mode 100644 index 63c615daa..000000000 --- a/hello-nextflow/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/main.nf b/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/main.nf deleted file mode 100644 index 7cbb7aba8..000000000 --- a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/main.nf +++ /dev/null @@ -1,38 +0,0 @@ -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" , emit: vcf - path "${cohort_name}.joint.vcf.idx" , emit: idx - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf b/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf deleted file mode 100644 index 6d9c40779..000000000 --- a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf +++ /dev/null @@ -1,1379 +0,0 @@ -##fileformat=VCFv4.2 -##ALT= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) -##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) -##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) -##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) -##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) -##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) -##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) -##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) -##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) -##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) -##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) -##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) -##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) -##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) -##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) -##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) -##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) -##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) -##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) -##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) -##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) -##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) -##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) -##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) -##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) -##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) -##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) -##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) -##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) -##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) -##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) -##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) -##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) -##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) -##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) -##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) -##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) -##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) -##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) -##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) -##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) -##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) -##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) -##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) -##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) -##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) -##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) -##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) -##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) -##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) -##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) -##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) -##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) -##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) -##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) -##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) -##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) -##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) -##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) -##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) -##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) -##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) -##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) -##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) -##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive) -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_father -20_10037292_10066351 3277 . G . . END=3281 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,120,1800 -20_10037292_10066351 3282 . T . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:45:95:45:0,95,1267 -20_10037292_10066351 3283 . T . . END=3300 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,112,1375 -20_10037292_10066351 3301 . C . . END=3301 GT:DP:GQ:MIN_DP:PL 0/0:52:88:52:0,88,1492 -20_10037292_10066351 3302 . T . . END=3307 GT:DP:GQ:MIN_DP:PL 0/0:51:99:49:0,112,1471 -20_10037292_10066351 3308 . A . . END=3308 GT:DP:GQ:MIN_DP:PL 0/0:49:84:49:0,84,1399 -20_10037292_10066351 3309 . A . . END=3437 GT:DP:GQ:MIN_DP:PL 0/0:47:99:41:0,107,1349 -20_10037292_10066351 3438 . T . . END=3447 GT:DP:GQ:MIN_DP:PL 0/0:41:90:38:0,90,1108 -20_10037292_10066351 3448 . T . . END=3449 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 3450 . A . . END=3450 GT:DP:GQ:MIN_DP:PL 0/0:35:50:35:0,50,880 -20_10037292_10066351 3451 . C . . END=3451 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 3452 . C . . END=3452 GT:DP:GQ:MIN_DP:PL 0/0:36:68:36:0,68,1042 -20_10037292_10066351 3453 . T . . END=3453 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 3454 . G . . END=3454 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,948 -20_10037292_10066351 3455 . T . . END=3458 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 -20_10037292_10066351 3459 . T . . END=3460 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 3461 . C . . END=3461 GT:DP:GQ:MIN_DP:PL 0/0:39:57:39:0,57,992 -20_10037292_10066351 3462 . T . . END=3462 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,99,1485 -20_10037292_10066351 3463 . G . . END=3463 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,910 -20_10037292_10066351 3464 . T . . END=3468 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 3469 . C . . END=3469 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,939 -20_10037292_10066351 3470 . T . . END=3472 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 3473 . T . . END=3473 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1129 -20_10037292_10066351 3474 . T . . END=3474 GT:DP:GQ:MIN_DP:PL 0/0:38:92:38:0,92,1102 -20_10037292_10066351 3475 . C . . END=3475 GT:DP:GQ:MIN_DP:PL 0/0:38:63:38:0,63,957 -20_10037292_10066351 3476 . T . . END=3478 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1197 -20_10037292_10066351 3479 . T . . END=3479 GT:DP:GQ:MIN_DP:PL 0/0:41:92:41:0,92,1155 -20_10037292_10066351 3480 . C CT, 359.60 . BaseQRankSum=0.220;DP=32;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=115200,32;ReadPosRankSum=-1.147 GT:AD:DP:GQ:PL:SB 0/1:15,16,0:31:99:367,0,375,412,423,835:6,9,9,7 -20_10037292_10066351 3481 . T . . END=3482 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3483 . T . . END=3483 GT:DP:GQ:MIN_DP:PL 0/0:32:65:32:0,65,949 -20_10037292_10066351 3484 . T . . END=3484 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3485 . T . . END=3487 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3488 . T . . END=3489 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,889 -20_10037292_10066351 3490 . C . . END=3490 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 3491 . A . . END=3491 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,996 -20_10037292_10066351 3492 . A . . END=3494 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 3495 . T . . END=3495 GT:DP:GQ:MIN_DP:PL 0/0:35:60:35:0,60,952 -20_10037292_10066351 3496 . A . . END=3497 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 3498 . A . . END=3498 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,937 -20_10037292_10066351 3499 . C . . END=3499 GT:DP:GQ:MIN_DP:PL 0/0:29:86:29:0,86,758 -20_10037292_10066351 3500 . G . . END=3500 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,646 -20_10037292_10066351 3501 . T . . END=3504 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 3505 . A . . END=3505 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,913 -20_10037292_10066351 3506 . C . . END=3506 GT:DP:GQ:MIN_DP:PL 0/0:31:45:31:0,45,739 -20_10037292_10066351 3507 . T . . END=3511 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3512 . A . . END=3512 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,994 -20_10037292_10066351 3513 . A . . END=3517 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 3518 . C . . END=3519 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,885 -20_10037292_10066351 3520 . AT A, 288.60 . BaseQRankSum=1.033;DP=34;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=122400,34;ReadPosRankSum=0.701 GT:AD:DP:GQ:PL:SB 0/1:18,13,0:31:99:296,0,424,350,463,813:8,10,7,6 -20_10037292_10066351 3522 . T . . END=3543 GT:DP:GQ:MIN_DP:PL 0/0:50:99:44:0,112,1347 -20_10037292_10066351 3544 . A . . END=3544 GT:DP:GQ:MIN_DP:PL 0/0:49:89:49:0,89,1374 -20_10037292_10066351 3545 . C . . END=3615 GT:DP:GQ:MIN_DP:PL 0/0:50:99:44:0,113,1172 -20_10037292_10066351 3616 . A . . END=3616 GT:DP:GQ:MIN_DP:PL 0/0:45:84:45:0,84,1268 -20_10037292_10066351 3617 . T . . END=3698 GT:DP:GQ:MIN_DP:PL 0/0:44:99:37:0,104,1096 -20_10037292_10066351 3699 . A . . END=3699 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1090 -20_10037292_10066351 3700 . G . . END=3701 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1116 -20_10037292_10066351 3702 . A . . END=3702 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1137 -20_10037292_10066351 3703 . T . . END=3704 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 3705 . G . . END=3705 GT:DP:GQ:MIN_DP:PL 0/0:40:85:40:0,85,1190 -20_10037292_10066351 3706 . G . . END=3710 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,114,1710 -20_10037292_10066351 3711 . G . . END=3711 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1263 -20_10037292_10066351 3712 . G . . END=3749 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,114,1209 -20_10037292_10066351 3750 . A . . END=3750 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1191 -20_10037292_10066351 3751 . A . . END=3865 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,100,1137 -20_10037292_10066351 3866 . G . . END=3866 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1117 -20_10037292_10066351 3867 . G . . END=3867 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3868 . T . . END=3868 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1109 -20_10037292_10066351 3869 . G . . END=3869 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3870 . T . . END=3870 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1088 -20_10037292_10066351 3871 . A . . END=3871 GT:DP:GQ:MIN_DP:PL 0/0:38:68:38:0,68,1086 -20_10037292_10066351 3872 . C . . END=3951 GT:DP:GQ:MIN_DP:PL 0/0:47:99:36:0,108,1151 -20_10037292_10066351 3952 . T . . END=3952 GT:DP:GQ:MIN_DP:PL 0/0:46:89:46:0,89,1351 -20_10037292_10066351 3953 . G . . END=4011 GT:DP:GQ:MIN_DP:PL 0/0:48:99:46:0,120,1800 -20_10037292_10066351 4012 . C T, 1432.06 . DP=47;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=169200,47 GT:AD:DP:GQ:PL:SB 1/1:0,46,0:46:99:1446,137,0,1446,137,1446:0,0,23,23 -20_10037292_10066351 4013 . G . . END=4035 GT:DP:GQ:MIN_DP:PL 0/0:48:99:42:0,108,1267 -20_10037292_10066351 4036 . T . . END=4036 GT:DP:GQ:MIN_DP:PL 0/0:43:95:43:0,95,1242 -20_10037292_10066351 4037 . T . . END=4060 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,104,1268 -20_10037292_10066351 4061 . A . . END=4061 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1217 -20_10037292_10066351 4062 . A . . END=4078 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,108,1620 -20_10037292_10066351 4079 . C . . END=4079 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1207 -20_10037292_10066351 4080 . A . . END=4121 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1157 -20_10037292_10066351 4122 . G . . END=4122 GT:DP:GQ:MIN_DP:PL 0/0:38:90:38:0,90,1137 -20_10037292_10066351 4123 . G . . END=4123 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 4124 . G . . END=4125 GT:DP:GQ:MIN_DP:PL 0/0:39:92:38:0,92,1088 -20_10037292_10066351 4126 . C . . END=4129 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,105,1575 -20_10037292_10066351 4130 . A . . END=4130 GT:DP:GQ:MIN_DP:PL 0/0:37:86:37:0,86,1018 -20_10037292_10066351 4131 . C . . END=4154 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1046 -20_10037292_10066351 4155 . T . . END=4155 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1137 -20_10037292_10066351 4156 . A . . END=4163 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1181 -20_10037292_10066351 4164 . T . . END=4164 GT:DP:GQ:MIN_DP:PL 0/0:40:97:40:0,97,1234 -20_10037292_10066351 4165 . A . . END=4177 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1088 -20_10037292_10066351 4178 . A . . END=4178 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1165 -20_10037292_10066351 4179 . T . . END=4198 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,99,1182 -20_10037292_10066351 4199 . G . . END=4201 GT:DP:GQ:MIN_DP:PL 0/0:39:96:37:0,96,1440 -20_10037292_10066351 4202 . G . . END=4204 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 4205 . T . . END=4217 GT:DP:GQ:MIN_DP:PL 0/0:34:93:32:0,93,1395 -20_10037292_10066351 4218 . G . . END=4218 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1030 -20_10037292_10066351 4219 . A . . END=4219 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 4220 . T . . END=4238 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1350 -20_10037292_10066351 4239 . C . . END=4240 GT:DP:GQ:MIN_DP:PL 0/0:34:66:33:0,66,924 -20_10037292_10066351 4241 . T . . END=4241 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 4242 . G . . END=4242 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,1040 -20_10037292_10066351 4243 . G . . END=4243 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,952 -20_10037292_10066351 4244 . T . . END=4244 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 4245 . T . . END=4245 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,968 -20_10037292_10066351 4246 . G . . END=4247 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 4248 . T . . END=4249 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,932 -20_10037292_10066351 4250 . G . . END=4250 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 4251 . T . . END=4252 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,904 -20_10037292_10066351 4253 . A . . END=4258 GT:DP:GQ:MIN_DP:PL 0/0:35:71:33:0,71,1001 -20_10037292_10066351 4259 . T . . END=4259 GT:DP:GQ:MIN_DP:PL 0/0:36:57:36:0,57,1051 -20_10037292_10066351 4260 . G . . END=4260 GT:DP:GQ:MIN_DP:PL 0/0:37:41:37:0,41,993 -20_10037292_10066351 4261 . G . . END=4261 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 4262 . T . . END=4263 GT:DP:GQ:MIN_DP:PL 0/0:36:71:35:0,71,1014 -20_10037292_10066351 4264 . T . . END=4264 GT:DP:GQ:MIN_DP:PL 0/0:37:62:37:0,62,1075 -20_10037292_10066351 4265 . G . . END=4265 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1050 -20_10037292_10066351 4266 . T . . END=4267 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1073 -20_10037292_10066351 4268 . T . . END=4271 GT:DP:GQ:MIN_DP:PL 0/0:37:75:37:0,75,1020 -20_10037292_10066351 4272 . A . . END=4272 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1090 -20_10037292_10066351 4273 . C . . END=4273 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1032 -20_10037292_10066351 4274 . C . . END=4274 GT:DP:GQ:MIN_DP:PL 0/0:38:48:38:0,48,1047 -20_10037292_10066351 4275 . A . . END=4287 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 4288 . T . . END=4288 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1099 -20_10037292_10066351 4289 . A . . END=4289 GT:DP:GQ:MIN_DP:PL 0/0:36:45:36:0,45,916 -20_10037292_10066351 4290 . T . . END=4290 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1107 -20_10037292_10066351 4291 . C . . END=4292 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4293 . G . . END=4293 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1065 -20_10037292_10066351 4294 . A . . END=4299 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4300 . G . . END=4304 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1058 -20_10037292_10066351 4305 . A . . END=4307 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 4308 . A . . END=4308 GT:DP:GQ:MIN_DP:PL 0/0:39:89:39:0,89,1179 -20_10037292_10066351 4309 . G . . END=4311 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 4312 . G . . END=4312 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1067 -20_10037292_10066351 4313 . G . . END=4318 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1130 -20_10037292_10066351 4319 . G . . END=4319 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1257 -20_10037292_10066351 4320 . A . . END=4326 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,105,1575 -20_10037292_10066351 4327 . A . . END=4327 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1145 -20_10037292_10066351 4328 . A . . END=4329 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,106,1200 -20_10037292_10066351 4330 . G . . END=4330 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1128 -20_10037292_10066351 4331 . A . . END=4334 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,107,1132 -20_10037292_10066351 4335 . A . . END=4336 GT:DP:GQ:MIN_DP:PL 0/0:38:94:38:0,94,1187 -20_10037292_10066351 4337 . A . . END=4337 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,114,1096 -20_10037292_10066351 4338 . C . . END=4338 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1117 -20_10037292_10066351 4339 . C . . END=4358 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,99,1173 -20_10037292_10066351 4359 . A . . END=4359 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1130 -20_10037292_10066351 4360 . G . . END=4360 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1244 -20_10037292_10066351 4361 . G . . END=4373 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,106,1101 -20_10037292_10066351 4374 . G . . END=4374 GT:DP:GQ:MIN_DP:PL 0/0:39:74:39:0,74,1076 -20_10037292_10066351 4375 . A . . END=4375 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1081 -20_10037292_10066351 4376 . T . . END=4380 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1077 -20_10037292_10066351 4381 . T . . END=4381 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1076 -20_10037292_10066351 4382 . T . . END=4382 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,101,1117 -20_10037292_10066351 4383 . T . . END=4383 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1096 -20_10037292_10066351 4384 . C . . END=4384 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1028 -20_10037292_10066351 4385 . A . . END=4385 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1150 -20_10037292_10066351 4386 . G . . END=4386 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1053 -20_10037292_10066351 4387 . A . . END=4387 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 4388 . C . . END=4388 GT:DP:GQ:MIN_DP:PL 0/0:39:78:39:0,78,1010 -20_10037292_10066351 4389 . C . . END=4394 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,983 -20_10037292_10066351 4395 . A . . END=4395 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1120 -20_10037292_10066351 4396 . G . . END=4403 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,107,1141 -20_10037292_10066351 4404 . A . . END=4404 GT:DP:GQ:MIN_DP:PL 0/0:42:59:42:0,59,935 -20_10037292_10066351 4405 . A . . END=4405 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,114,1710 -20_10037292_10066351 4406 . C . . END=4406 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 4407 . A . . END=4408 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,939 -20_10037292_10066351 4409 . A ATG,ATATG, 955.03 . DP=34;ExcessHet=0.0000;MLEAC=0,2,0;MLEAF=0.00,1.00,0.00;RAW_MQandDP=122400,34 GT:AD:DP:GQ:PL:SB 2/2:0,0,28,0:28:90:969,998,1257,90,96,0,1003,1147,100,1113:0,0,9,19 -20_10037292_10066351 4410 . T . . END=4423 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 4424 . T . . END=4424 GT:DP:GQ:MIN_DP:PL 0/0:32:72:32:0,72,959 -20_10037292_10066351 4425 . G . . END=4431 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4432 . T . . END=4432 GT:DP:GQ:MIN_DP:PL 0/0:32:65:32:0,65,948 -20_10037292_10066351 4433 . G . . END=4435 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 4436 . C . . END=4436 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,943 -20_10037292_10066351 4437 . A . . END=4437 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4438 . T . . END=4443 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 4444 . T . . END=4450 GT:DP:GQ:MIN_DP:PL 0/0:33:84:28:0,84,723 -20_10037292_10066351 4451 . G . . END=4451 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 4452 . T . . END=4459 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 4460 . T . . END=4460 GT:DP:GQ:MIN_DP:PL 0/0:32:75:32:0,75,1125 -20_10037292_10066351 4461 . A . . END=4461 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 4462 . T . . END=4463 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 4464 . T TA, 621.60 . BaseQRankSum=0.108;DP=33;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=118800,33;ReadPosRankSum=1.266 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:15,17,0:32:99:0|1:4464_T_TA:629,0,554,674,605,1280:4464:6,9,6,11 -20_10037292_10066351 4465 . T TA, 621.60 . BaseQRankSum=-0.225;DP=32;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=115200,32;ReadPosRankSum=0.910 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:15,17,0:32:99:0|1:4464_T_TA:629,0,554,674,605,1280:4464:6,9,6,11 -20_10037292_10066351 4466 . T . . END=4467 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 4468 . T . . END=4472 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,1485 -20_10037292_10066351 4473 . G . . END=4473 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1021 -20_10037292_10066351 4474 . A . . END=4476 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,105,994 -20_10037292_10066351 4477 . C . . END=4477 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,963 -20_10037292_10066351 4478 . A . . END=4481 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1046 -20_10037292_10066351 4482 . T . . END=4492 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,981 -20_10037292_10066351 4493 . G . . END=4495 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,945 -20_10037292_10066351 4496 . G . . END=4496 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4497 . T . . END=4503 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 -20_10037292_10066351 4504 . A . . END=4504 GT:DP:GQ:MIN_DP:PL 0/0:30:61:30:0,61,825 -20_10037292_10066351 4505 . T . . END=4512 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4513 . C . . END=4514 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,812 -20_10037292_10066351 4515 . T . . END=4519 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 4520 . A . . END=4520 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,822 -20_10037292_10066351 4521 . C . . END=4521 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,799 -20_10037292_10066351 4522 . C . . END=4524 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 4525 . C . . END=4533 GT:DP:GQ:MIN_DP:PL 0/0:27:62:25:0,62,779 -20_10037292_10066351 4534 . G . . END=4534 GT:DP:GQ:MIN_DP:PL 0/0:25:57:25:0,57,722 -20_10037292_10066351 4535 . G . . END=4535 GT:DP:GQ:MIN_DP:PL 0/0:25:63:25:0,63,945 -20_10037292_10066351 4536 . T . . END=4541 GT:DP:GQ:MIN_DP:PL 0/0:23:57:22:0,57,855 -20_10037292_10066351 4542 . A . . END=4544 GT:DP:GQ:MIN_DP:PL 0/0:24:63:24:0,63,945 -20_10037292_10066351 4545 . T . . END=4545 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,644 -20_10037292_10066351 4546 . T . . END=4550 GT:DP:GQ:MIN_DP:PL 0/0:24:61:23:0,61,673 -20_10037292_10066351 4551 . T . . END=4551 GT:DP:GQ:MIN_DP:PL 0/0:25:42:25:0,42,739 -20_10037292_10066351 4552 . G . . END=4563 GT:DP:GQ:MIN_DP:PL 0/0:24:69:23:0,69,660 -20_10037292_10066351 4564 . C . . END=4564 GT:DP:GQ:MIN_DP:PL 0/0:22:48:22:0,48,565 -20_10037292_10066351 4565 . G . . END=4567 GT:DP:GQ:MIN_DP:PL 0/0:24:63:22:0,63,580 -20_10037292_10066351 4568 . T . . END=4568 GT:DP:GQ:MIN_DP:PL 0/0:24:59:24:0,59,679 -20_10037292_10066351 4569 . T . . END=4572 GT:DP:GQ:MIN_DP:PL 0/0:25:61:24:0,61,691 -20_10037292_10066351 4573 . G . . END=4573 GT:DP:GQ:MIN_DP:PL 0/0:25:45:25:0,45,636 -20_10037292_10066351 4574 . T . . END=4577 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,731 -20_10037292_10066351 4578 . T . . END=4584 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,692 -20_10037292_10066351 4585 . G . . END=4585 GT:DP:GQ:MIN_DP:PL 0/0:23:69:23:0,69,678 -20_10037292_10066351 4586 . A . . END=4586 GT:DP:GQ:MIN_DP:PL 0/0:24:53:24:0,53,694 -20_10037292_10066351 4587 . G . . END=4604 GT:DP:GQ:MIN_DP:PL 0/0:24:60:24:0,60,642 -20_10037292_10066351 4605 . T . . END=4605 GT:DP:GQ:MIN_DP:PL 0/0:24:54:24:0,54,810 -20_10037292_10066351 4606 . G . . END=4609 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 -20_10037292_10066351 4610 . A . . END=4612 GT:DP:GQ:MIN_DP:PL 0/0:24:54:21:0,54,810 -20_10037292_10066351 4613 . C . . END=4613 GT:DP:GQ:MIN_DP:PL 0/0:22:50:22:0,50,605 -20_10037292_10066351 4614 . T . . END=4616 GT:DP:GQ:MIN_DP:PL 0/0:23:54:21:0,54,810 -20_10037292_10066351 4617 . T . . END=4617 GT:DP:GQ:MIN_DP:PL 0/0:21:49:21:0,49,590 -20_10037292_10066351 4618 . C . . END=4618 GT:DP:GQ:MIN_DP:PL 0/0:21:36:21:0,36,562 -20_10037292_10066351 4619 . T . . END=4619 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 -20_10037292_10066351 4620 . C . . END=4620 GT:DP:GQ:MIN_DP:PL 0/0:19:37:19:0,37,499 -20_10037292_10066351 4621 . G . . END=4626 GT:DP:GQ:MIN_DP:PL 0/0:19:54:18:0,54,532 -20_10037292_10066351 4627 . C . . END=4627 GT:DP:GQ:MIN_DP:PL 0/0:19:24:19:0,24,493 -20_10037292_10066351 4628 . T . . END=4628 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20_10037292_10066351 4629 . G . . END=4629 GT:DP:GQ:MIN_DP:PL 0/0:19:42:19:0,42,568 -20_10037292_10066351 4630 . A . . END=4631 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20_10037292_10066351 4632 . C . . END=4632 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 -20_10037292_10066351 4633 . T . . END=4633 GT:DP:GQ:MIN_DP:PL 0/0:20:48:20:0,48,592 -20_10037292_10066351 4634 . C . . END=4634 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 -20_10037292_10066351 4635 . A . . END=4638 GT:DP:GQ:MIN_DP:PL 0/0:24:66:23:0,66,990 -20_10037292_10066351 4639 . G . . END=4639 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,667 -20_10037292_10066351 4640 . A . . END=4641 GT:DP:GQ:MIN_DP:PL 0/0:23:56:23:0,56,654 -20_10037292_10066351 4642 . C . . END=4644 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4645 . C . . END=4649 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,763 -20_10037292_10066351 4650 . T . . END=4650 GT:DP:GQ:MIN_DP:PL 0/0:26:64:26:0,64,757 -20_10037292_10066351 4651 . T . . END=4657 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 4658 . C . . END=4658 GT:DP:GQ:MIN_DP:PL 0/0:26:61:26:0,61,781 -20_10037292_10066351 4659 . C . . END=4660 GT:DP:GQ:MIN_DP:PL 0/0:28:80:27:0,80,793 -20_10037292_10066351 4661 . A . . END=4661 GT:DP:GQ:MIN_DP:PL 0/0:28:73:28:0,73,846 -20_10037292_10066351 4662 . A . . END=4664 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,870 -20_10037292_10066351 4665 . T . . END=4665 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,787 -20_10037292_10066351 4666 . A . . END=4666 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,793 -20_10037292_10066351 4667 . C . . END=4670 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,917 -20_10037292_10066351 4671 . G . . END=4671 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,880 -20_10037292_10066351 4672 . A . . END=4679 GT:DP:GQ:MIN_DP:PL 0/0:30:87:29:0,87,909 -20_10037292_10066351 4680 . T . . END=4680 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,985 -20_10037292_10066351 4681 . G . . END=4681 GT:DP:GQ:MIN_DP:PL 0/0:31:65:31:0,65,862 -20_10037292_10066351 4682 . T . . END=4682 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,981 -20_10037292_10066351 4683 . G . . END=4683 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,948 -20_10037292_10066351 4684 . A . . END=4691 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 4692 . C . . END=4697 GT:DP:GQ:MIN_DP:PL 0/0:29:78:27:0,78,1170 -20_10037292_10066351 4698 . G . . END=4701 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 4702 . T . . END=4706 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,928 -20_10037292_10066351 4707 . A . . END=4720 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,921 -20_10037292_10066351 4721 . T . . END=4721 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,937 -20_10037292_10066351 4722 . C . . END=4727 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 4728 . A . . END=4734 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 4735 . T . . END=4735 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1021 -20_10037292_10066351 4736 . A . . END=4736 GT:DP:GQ:MIN_DP:PL 0/0:33:70:33:0,70,940 -20_10037292_10066351 4737 . C . . END=4739 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 4740 . T . . END=4740 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,989 -20_10037292_10066351 4741 . A . . END=4745 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 4746 . G . . END=4754 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4755 . A . . END=4755 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,991 -20_10037292_10066351 4756 . A . . END=4760 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 4761 . A . . END=4761 GT:DP:GQ:MIN_DP:PL 0/0:37:74:37:0,74,1046 -20_10037292_10066351 4762 . G . . END=4762 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1043 -20_10037292_10066351 4763 . A . . END=4768 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1087 -20_10037292_10066351 4769 . G . . END=4769 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1036 -20_10037292_10066351 4770 . A . . END=4772 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 4773 . A . . END=4774 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1041 -20_10037292_10066351 4775 . T . . END=4775 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 4776 . C . . END=4778 GT:DP:GQ:MIN_DP:PL 0/0:39:96:38:0,96,1440 -20_10037292_10066351 4779 . T . . END=4779 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 4780 . A . . END=4780 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 4781 . T . . END=4789 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1485 -20_10037292_10066351 4790 . A . . END=4791 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 4792 . A . . END=4807 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1070 -20_10037292_10066351 4808 . C . . END=4808 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1087 -20_10037292_10066351 4809 . A . . END=4810 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1167 -20_10037292_10066351 4811 . T . . END=4811 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1048 -20_10037292_10066351 4812 . A . . END=4817 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4818 . C . . END=4818 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1096 -20_10037292_10066351 4819 . C . . END=4855 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,102,1195 -20_10037292_10066351 4856 . T . . END=4856 GT:DP:GQ:MIN_DP:PL 0/0:44:90:44:0,90,1268 -20_10037292_10066351 4857 . A . . END=4893 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,99,1256 -20_10037292_10066351 4894 . C . . END=4894 GT:DP:GQ:MIN_DP:PL 0/0:44:83:44:0,83,1313 -20_10037292_10066351 4895 . T . . END=4974 GT:DP:GQ:MIN_DP:PL 0/0:44:99:40:0,107,1201 -20_10037292_10066351 4975 . T . . END=4975 GT:DP:GQ:MIN_DP:PL 0/0:43:81:43:0,81,1251 -20_10037292_10066351 4976 . A . . END=4986 GT:DP:GQ:MIN_DP:PL 0/0:43:99:39:0,105,1575 -20_10037292_10066351 4987 . A . . END=4990 GT:DP:GQ:MIN_DP:PL 0/0:38:93:37:0,93,1395 -20_10037292_10066351 4991 . C . . END=4992 GT:DP:GQ:MIN_DP:PL 0/0:37:87:36:0,87,1305 -20_10037292_10066351 4993 . G . . END=4994 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 4995 . G . . END=4995 GT:DP:GQ:MIN_DP:PL 0/0:36:89:36:0,89,1095 -20_10037292_10066351 4996 . G . . END=5001 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 5002 . T . . END=5002 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,916 -20_10037292_10066351 5003 . T . . END=5005 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 5006 . G . . END=5006 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1068 -20_10037292_10066351 5007 . A . . END=5008 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 5009 . C . . END=5016 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5017 . G . . END=5017 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 5018 . G . . END=5026 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 5027 . C T, 1150.06 . DP=37;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=133200,37 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:1164,108,0,1164,108,1164:0,0,19,17 -20_10037292_10066351 5028 . C . . END=5034 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1206 -20_10037292_10066351 5035 . A . . END=5035 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1168 -20_10037292_10066351 5036 . T . . END=5045 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1179 -20_10037292_10066351 5046 . A . . END=5046 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1162 -20_10037292_10066351 5047 . G . . END=5055 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,101,1171 -20_10037292_10066351 5056 . G . . END=5056 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1102 -20_10037292_10066351 5057 . A . . END=5058 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1142 -20_10037292_10066351 5059 . G . . END=5061 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1117 -20_10037292_10066351 5062 . T . . END=5064 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 5065 . A . . END=5065 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1130 -20_10037292_10066351 5066 . A . . END=5066 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 5067 . C . . END=5067 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1147 -20_10037292_10066351 5068 . C . . END=5068 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,111,1665 -20_10037292_10066351 5069 . A . . END=5071 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1159 -20_10037292_10066351 5072 . G . . END=5072 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,103,1233 -20_10037292_10066351 5073 . A . . END=5073 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1186 -20_10037292_10066351 5074 . G . . END=5074 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,101,1226 -20_10037292_10066351 5075 . G . . END=5075 GT:DP:GQ:MIN_DP:PL 0/0:40:75:40:0,75,1121 -20_10037292_10066351 5076 . T . . END=5079 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,104,1188 -20_10037292_10066351 5080 . T . . END=5080 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1172 -20_10037292_10066351 5081 . C . . END=5125 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,102,1196 -20_10037292_10066351 5126 . A . . END=5126 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1147 -20_10037292_10066351 5127 . G . . END=5127 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 5128 . T . . END=5128 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1099 -20_10037292_10066351 5129 . C . . END=5187 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1143 -20_10037292_10066351 5188 . G . . END=5188 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1135 -20_10037292_10066351 5189 . G . . END=5190 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1149 -20_10037292_10066351 5191 . G . . END=5191 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1167 -20_10037292_10066351 5192 . G . . END=5193 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,111,1665 -20_10037292_10066351 5194 . T . . END=5194 GT:DP:GQ:MIN_DP:PL 0/0:39:85:39:0,85,1200 -20_10037292_10066351 5195 . C . . END=5228 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,102,1180 -20_10037292_10066351 5229 . T . . END=5229 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1052 -20_10037292_10066351 5230 . A . . END=5237 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,102,1168 -20_10037292_10066351 5238 . G . . END=5238 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1187 -20_10037292_10066351 5239 . C . . END=5249 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 5250 . A . . END=5254 GT:DP:GQ:MIN_DP:PL 0/0:37:96:35:0,96,1440 -20_10037292_10066351 5255 . C . . END=5262 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5263 . T . . END=5263 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,998 -20_10037292_10066351 5264 . G . . END=5271 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1013 -20_10037292_10066351 5272 . C . . END=5275 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 5276 . T . . END=5278 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5279 . T . . END=5281 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,983 -20_10037292_10066351 5282 . A . . END=5315 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,99,1161 -20_10037292_10066351 5316 . A . . END=5323 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 5324 . C . . END=5324 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1014 -20_10037292_10066351 5325 . A . . END=5334 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 5335 . G . . END=5337 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,992 -20_10037292_10066351 5338 . C . . END=5341 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 5342 . G . . END=5342 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,954 -20_10037292_10066351 5343 . T . . END=5344 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,1005 -20_10037292_10066351 5345 . C . . END=5345 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,988 -20_10037292_10066351 5346 . A . . END=5346 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1105 -20_10037292_10066351 5347 . G . . END=5347 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 5348 . G . . END=5349 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1004 -20_10037292_10066351 5350 . G . . END=5350 GT:DP:GQ:MIN_DP:PL 0/0:34:52:34:0,52,932 -20_10037292_10066351 5351 . C . . END=5351 GT:DP:GQ:MIN_DP:PL 0/0:34:46:34:0,46,977 -20_10037292_10066351 5352 . A . . END=5353 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1000 -20_10037292_10066351 5354 . A . . END=5354 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1002 -20_10037292_10066351 5355 . A . . END=5355 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5356 . T . . END=5358 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 5359 . C . . END=5359 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1003 -20_10037292_10066351 5360 . A . . END=5361 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1086 -20_10037292_10066351 5362 . A . . END=5364 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 5365 . G . . END=5365 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1083 -20_10037292_10066351 5366 . T . . END=5366 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 5367 . G . . END=5367 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 5368 . A . . END=5369 GT:DP:GQ:MIN_DP:PL 0/0:35:85:34:0,85,965 -20_10037292_10066351 5370 . T . . END=5370 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 5371 . C . . END=5371 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1033 -20_10037292_10066351 5372 . C . . END=5372 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,980 -20_10037292_10066351 5373 . T . . END=5374 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 5375 . G . . END=5376 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 5377 . G . . END=5383 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,937 -20_10037292_10066351 5384 . T . . END=5388 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,888 -20_10037292_10066351 5389 . T . . END=5394 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 5395 . A . . END=5395 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,896 -20_10037292_10066351 5396 . C . . END=5400 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 5401 . T . . END=5401 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,835 -20_10037292_10066351 5402 . T . . END=5402 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 5403 . T . . END=5403 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,901 -20_10037292_10066351 5404 . T . . END=5404 GT:DP:GQ:MIN_DP:PL 0/0:31:68:31:0,68,872 -20_10037292_10066351 5405 . T . . END=5405 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 5406 . A . . END=5406 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,986 -20_10037292_10066351 5407 . A . . END=5417 GT:DP:GQ:MIN_DP:PL 0/0:39:99:34:0,99,1485 -20_10037292_10066351 5418 . A . . END=5418 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 5419 . A . . END=5419 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1140 -20_10037292_10066351 5420 . C . . END=5422 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 5423 . C . . END=5435 GT:DP:GQ:MIN_DP:PL 0/0:40:99:36:0,99,1485 -20_10037292_10066351 5436 . A . . END=5436 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1058 -20_10037292_10066351 5437 . A . . END=5437 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1088 -20_10037292_10066351 5438 . C . . END=5440 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 5441 . G . . END=5441 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1044 -20_10037292_10066351 5442 . C . . END=5442 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 5443 . C . . END=5443 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1064 -20_10037292_10066351 5444 . T . . END=5446 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5447 . T . . END=5447 GT:DP:GQ:MIN_DP:PL 0/0:37:89:37:0,89,1070 -20_10037292_10066351 5448 . T . . END=5453 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 5454 . G . . END=5454 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1131 -20_10037292_10066351 5455 . A . . END=5468 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,105,1273 -20_10037292_10066351 5469 . A G, 545.64 . BaseQRankSum=-3.665;DP=42;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=151200,42;ReadPosRankSum=1.500 GT:AD:DP:GQ:PL:SB 0/1:18,23,0:41:99:553,0,486,607,555,1162:12,6,14,9 -20_10037292_10066351 5470 . G . . END=5486 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,117,1755 -20_10037292_10066351 5487 . A . . END=5487 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1225 -20_10037292_10066351 5488 . A . . END=5495 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1203 -20_10037292_10066351 7536 . C . . END=7551 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,1485 -20_10037292_10066351 7552 . T . . END=7552 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1073 -20_10037292_10066351 7553 . A . . END=7555 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 7556 . C . . END=7556 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,991 -20_10037292_10066351 7557 . A G, 305.64 . BaseQRankSum=-1.362;DP=37;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=133200,37;ReadPosRankSum=1.111 GT:AD:DP:GQ:PL:SB 0/1:19,15,0:34:99:313,0,493,370,538,907:11,8,8,7 -20_10037292_10066351 7558 . C . . END=7558 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 7559 . T . . END=7578 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1485 -20_10037292_10066351 7579 . T . . END=7579 GT:DP:GQ:MIN_DP:PL 0/0:38:92:38:0,92,1186 -20_10037292_10066351 7580 . C . . END=7582 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 7583 . C . . END=7583 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1177 -20_10037292_10066351 7584 . A . . END=7586 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 7587 . T . . END=7587 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1163 -20_10037292_10066351 7588 . T . . END=7599 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,100,1167 -20_10037292_10066351 7600 . C . . END=7600 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1131 -20_10037292_10066351 7601 . C . . END=7612 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,101,1205 -20_10037292_10066351 7613 . T . . END=7613 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1175 -20_10037292_10066351 7614 . C . . END=7617 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,111,1229 -20_10037292_10066351 7618 . G . . END=7618 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1191 -20_10037292_10066351 7619 . T . . END=7619 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 7620 . A . . END=7620 GT:DP:GQ:MIN_DP:PL 0/0:38:92:38:0,92,1159 -20_10037292_10066351 7621 . T . . END=7621 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1233 -20_10037292_10066351 7622 . A . . END=7622 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1202 -20_10037292_10066351 7623 . T . . END=7634 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1213 -20_10037292_10066351 7635 . G . . END=7635 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1213 -20_10037292_10066351 7636 . G . . END=7640 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,105,1575 -20_10037292_10066351 7641 . T . . END=7641 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1158 -20_10037292_10066351 7642 . T . . END=7643 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 7644 . A . . END=7644 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1085 -20_10037292_10066351 7645 . T . . END=7652 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,105,1140 -20_10037292_10066351 7653 . A . . END=7653 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 7654 . G . . END=7656 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 7657 . A . . END=7661 GT:DP:GQ:MIN_DP:PL 0/0:39:93:39:0,93,1395 -20_10037292_10066351 7662 . G . . END=7666 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 7667 . A . . END=7667 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,992 -20_10037292_10066351 7668 . C . . END=7681 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1088 -20_10037292_10066351 7682 . C . . END=7682 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1110 -20_10037292_10066351 7683 . C . . END=7689 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1530 -20_10037292_10066351 7690 . A . . END=7690 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1015 -20_10037292_10066351 7691 . C . . END=7700 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 7701 . A . . END=7705 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 7706 . C . . END=7706 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1305 -20_10037292_10066351 7707 . A . . END=7713 GT:DP:GQ:MIN_DP:PL 0/0:37:90:34:0,90,1350 -20_10037292_10066351 7714 . A . . END=7714 GT:DP:GQ:MIN_DP:PL 0/0:36:89:36:0,89,1115 -20_10037292_10066351 7715 . C . . END=7715 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 7716 . A . . END=7716 GT:DP:GQ:MIN_DP:PL 0/0:36:89:36:0,89,1160 -20_10037292_10066351 7717 . G . . END=7717 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7718 . T . . END=7719 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 7720 . C . . END=7720 GT:DP:GQ:MIN_DP:PL 0/0:34:83:34:0,83,1055 -20_10037292_10066351 7721 . T . . END=7722 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 7723 . A . . END=7723 GT:DP:GQ:MIN_DP:PL 0/0:34:66:34:0,66,975 -20_10037292_10066351 7724 . A . . END=7724 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,1060 -20_10037292_10066351 7725 . C . . END=7725 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7726 . A . . END=7726 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1088 -20_10037292_10066351 7727 . A . . END=7728 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1073 -20_10037292_10066351 7729 . G . . END=7729 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1042 -20_10037292_10066351 7730 . T . . END=7731 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 7732 . G . . END=7732 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1019 -20_10037292_10066351 7733 . A . . END=7740 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 7741 . A . . END=7745 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 7746 . G . . END=7748 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,979 -20_10037292_10066351 7749 . T . . END=7750 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1024 -20_10037292_10066351 7751 . C . . END=7751 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,992 -20_10037292_10066351 7752 . C . . END=7753 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 7754 . C . . END=7754 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,964 -20_10037292_10066351 7755 . C . . END=7755 GT:DP:GQ:MIN_DP:PL 0/0:33:58:33:0,58,922 -20_10037292_10066351 7756 . A . . END=7761 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 7762 . A . . END=7762 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,973 -20_10037292_10066351 7763 . T . . END=7767 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,888 -20_10037292_10066351 7768 . A . . END=7769 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7770 . C . . END=7771 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1081 -20_10037292_10066351 7772 . T . . END=7776 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1120 -20_10037292_10066351 7777 . T . . END=7777 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1094 -20_10037292_10066351 7778 . A . . END=7785 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1159 -20_10037292_10066351 7786 . G T, 1052.06 . DP=35;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=126000,35 GT:AD:DP:GQ:PL:SB 1/1:0,34,0:34:99:1066,102,0,1066,102,1066:0,0,8,26 -20_10037292_10066351 7787 . C . . END=7788 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 7789 . C . . END=7789 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1118 -20_10037292_10066351 7790 . A . . END=7790 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,111,1665 -20_10037292_10066351 7791 . T . . END=7791 GT:DP:GQ:MIN_DP:PL 0/0:41:85:41:0,85,1172 -20_10037292_10066351 7792 . T . . END=7813 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,105,1215 -20_10037292_10066351 7814 . T . . END=7814 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1167 -20_10037292_10066351 7815 . T . . END=7820 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1665 -20_10037292_10066351 7821 . T . . END=7821 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1114 -20_10037292_10066351 7822 . T . . END=7822 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 7823 . A . . END=7823 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1129 -20_10037292_10066351 7824 . C . . END=7837 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1123 -20_10037292_10066351 7838 . C . . END=7838 GT:DP:GQ:MIN_DP:PL 0/0:39:70:39:0,70,1119 -20_10037292_10066351 7839 . A . . END=7844 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1164 -20_10037292_10066351 7845 . C . . END=7846 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1123 -20_10037292_10066351 7847 . C . . END=7854 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,108,1620 -20_10037292_10066351 7855 . A . . END=7857 GT:DP:GQ:MIN_DP:PL 0/0:39:82:39:0,82,1089 -20_10037292_10066351 7858 . C . . END=7861 GT:DP:GQ:MIN_DP:PL 0/0:38:75:37:0,75,1065 -20_10037292_10066351 7862 . G . . END=7862 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1123 -20_10037292_10066351 7863 . G . . END=7865 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1124 -20_10037292_10066351 7866 . T . . END=7866 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1129 -20_10037292_10066351 7867 . A . . END=7884 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,101,1090 -20_10037292_10066351 7885 . G . . END=7885 GT:DP:GQ:MIN_DP:PL 0/0:41:94:41:0,94,1227 -20_10037292_10066351 7886 . G . . END=7897 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,110,1179 -20_10037292_10066351 7898 . T . . END=7898 GT:DP:GQ:MIN_DP:PL 0/0:41:59:41:0,59,1084 -20_10037292_10066351 7899 . A . . END=7913 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1236 -20_10037292_10066351 7914 . T . . END=7914 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 7915 . T . . END=7915 GT:DP:GQ:MIN_DP:PL 0/0:39:82:39:0,82,1146 -20_10037292_10066351 7916 . A . . END=7927 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1485 -20_10037292_10066351 7928 . C . . END=7928 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1114 -20_10037292_10066351 7929 . A . . END=7930 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 7931 . A . . END=7934 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 7935 . G . . END=7935 GT:DP:GQ:MIN_DP:PL 0/0:37:75:37:0,75,1128 -20_10037292_10066351 7936 . G . . END=7941 GT:DP:GQ:MIN_DP:PL 0/0:38:90:35:0,90,1350 -20_10037292_10066351 7942 . T . . END=7942 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,979 -20_10037292_10066351 7943 . T . . END=7945 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 7946 . C . . END=7946 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 7947 . A . . END=7948 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 7949 . T . . END=7956 GT:DP:GQ:MIN_DP:PL 0/0:31:80:30:0,80,971 -20_10037292_10066351 7957 . T . . END=7957 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,897 -20_10037292_10066351 7958 . G . . END=7981 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,888 -20_10037292_10066351 7982 . A . . END=7984 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 7985 . A . . END=7985 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 7986 . G . . END=7991 GT:DP:GQ:MIN_DP:PL 0/0:30:77:29:0,77,809 -20_10037292_10066351 7992 . A . . END=8000 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8001 . G . . END=8009 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,855 -20_10037292_10066351 8010 . G . . END=8021 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 8022 . T . . END=8022 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,890 -20_10037292_10066351 8023 . T . . END=8023 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8024 . G . . END=8024 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,900 -20_10037292_10066351 8025 . A . . END=8026 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 8027 . T . . END=8027 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,870 -20_10037292_10066351 8028 . A . . END=8034 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 8035 . G . . END=8037 GT:DP:GQ:MIN_DP:PL 0/0:28:73:28:0,73,921 -20_10037292_10066351 8038 . G . . END=8038 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8039 . C . . END=8039 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,822 -20_10037292_10066351 8040 . A . . END=8041 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8042 . T . . END=8042 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,842 -20_10037292_10066351 8043 . T . . END=8045 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8046 . C . . END=8046 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,780 -20_10037292_10066351 8047 . A . . END=8047 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8048 . G . . END=8050 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8051 . C . . END=8051 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,745 -20_10037292_10066351 8052 . A . . END=8054 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 8055 . C . . END=8055 GT:DP:GQ:MIN_DP:PL 0/0:29:63:29:0,63,853 -20_10037292_10066351 8056 . C . . END=8056 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,837 -20_10037292_10066351 8057 . C . . END=8057 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8058 . A . . END=8059 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,844 -20_10037292_10066351 8060 . T . . END=8060 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 8061 . C . . END=8061 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20_10037292_10066351 8062 . C . . END=8062 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,798 -20_10037292_10066351 8063 . A . . END=8073 GT:DP:GQ:MIN_DP:PL 0/0:30:71:27:0,71,849 -20_10037292_10066351 8074 . T . . END=8074 GT:DP:GQ:MIN_DP:PL 0/0:25:43:25:0,43,699 -20_10037292_10066351 8075 . A . . END=8075 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,812 -20_10037292_10066351 8076 . A . . END=8076 GT:DP:GQ:MIN_DP:PL 0/0:26:47:26:0,47,685 -20_10037292_10066351 8077 . A . . END=8077 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8078 . A . . END=8078 GT:DP:GQ:MIN_DP:PL 0/0:26:66:26:0,66,773 -20_10037292_10066351 8079 . G . . END=8079 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8080 . C . . END=8080 GT:DP:GQ:MIN_DP:PL 0/0:26:31:26:0,31,667 -20_10037292_10066351 8081 . A . . END=8081 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8082 . A . . END=8082 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8083 . T . . END=8083 GT:DP:GQ:MIN_DP:PL 0/0:28:37:28:0,37,743 -20_10037292_10066351 8084 . G . . END=8084 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8085 . T . . END=8085 GT:DP:GQ:MIN_DP:PL 0/0:28:25:28:0,25,743 -20_10037292_10066351 8086 . G . . END=8086 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,783 -20_10037292_10066351 8087 . A . . END=8087 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,773 -20_10037292_10066351 8088 . C . . END=8088 GT:DP:GQ:MIN_DP:PL 0/0:28:25:28:0,25,675 -20_10037292_10066351 8089 . A . . END=8089 GT:DP:GQ:MIN_DP:PL 0/0:28:50:28:0,50,799 -20_10037292_10066351 8090 . A . . END=8090 GT:DP:GQ:MIN_DP:PL 0/0:28:64:28:0,64,842 -20_10037292_10066351 8091 . G . . END=8091 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8092 . A . . END=8092 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8093 . A . . END=8093 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8094 . A . . END=8095 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,881 -20_10037292_10066351 8096 . A . . END=8098 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 8099 . T . . END=8099 GT:DP:GQ:MIN_DP:PL 0/0:29:58:29:0,58,810 -20_10037292_10066351 8100 . A . . END=8101 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8102 . A . . END=8105 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,888 -20_10037292_10066351 8106 . T . . END=8106 GT:DP:GQ:MIN_DP:PL 0/0:28:50:28:0,50,808 -20_10037292_10066351 8107 . G . . END=8107 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,829 -20_10037292_10066351 8108 . G . . END=8108 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8109 . T . . END=8110 GT:DP:GQ:MIN_DP:PL 0/0:28:64:27:0,64,791 -20_10037292_10066351 8111 . A . . END=8111 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8112 . G . . END=8112 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,816 -20_10037292_10066351 8113 . G . . END=8113 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8114 . G . . END=8114 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,659 -20_10037292_10066351 8115 . A . . END=8115 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 8116 . A . . END=8116 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,663 -20_10037292_10066351 8117 . A . . END=8117 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8118 . A . . END=8118 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,791 -20_10037292_10066351 8119 . G . . END=8119 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,801 -20_10037292_10066351 8120 . A . . END=8120 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 8121 . G . . END=8121 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,817 -20_10037292_10066351 8122 . G . . END=8122 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8123 . C . . END=8123 GT:DP:GQ:MIN_DP:PL 0/0:27:52:27:0,52,788 -20_10037292_10066351 8124 . C . . END=8125 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,1035 -20_10037292_10066351 8126 . A . . END=8126 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8127 . A . . END=8128 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,1035 -20_10037292_10066351 8129 . C . . END=8129 GT:DP:GQ:MIN_DP:PL 0/0:27:54:27:0,54,786 -20_10037292_10066351 8130 . C . . END=8130 GT:DP:GQ:MIN_DP:PL 0/0:27:33:27:0,33,742 -20_10037292_10066351 8131 . A . . END=8133 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 8134 . T . . END=8134 GT:DP:GQ:MIN_DP:PL 0/0:25:44:25:0,44,709 -20_10037292_10066351 8135 . C . . END=8135 GT:DP:GQ:MIN_DP:PL 0/0:26:47:26:0,47,776 -20_10037292_10066351 8136 . C . . END=8136 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8137 . T . . END=8137 GT:DP:GQ:MIN_DP:PL 0/0:26:33:26:0,33,726 -20_10037292_10066351 8138 . G . . END=8138 GT:DP:GQ:MIN_DP:PL 0/0:25:48:25:0,48,757 -20_10037292_10066351 8139 . G . . END=8139 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,789 -20_10037292_10066351 8140 . A . . END=8141 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8142 . A . . END=8142 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,835 -20_10037292_10066351 8143 . G . . END=8143 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 8144 . A . . END=8144 GT:DP:GQ:MIN_DP:PL 0/0:28:51:28:0,51,816 -20_10037292_10066351 8145 . T . . END=8145 GT:DP:GQ:MIN_DP:PL 0/0:28:61:28:0,61,806 -20_10037292_10066351 8146 . T . . END=8146 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 8147 . T . . END=8147 GT:DP:GQ:MIN_DP:PL 0/0:28:47:28:0,47,801 -20_10037292_10066351 8148 . G . . END=8149 GT:DP:GQ:MIN_DP:PL 0/0:29:75:28:0,75,871 -20_10037292_10066351 8150 . A . . END=8151 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,887 -20_10037292_10066351 8152 . G . . END=8153 GT:DP:GQ:MIN_DP:PL 0/0:30:64:30:0,64,889 -20_10037292_10066351 8154 . C . . END=8154 GT:DP:GQ:MIN_DP:PL 0/0:29:58:29:0,58,820 -20_10037292_10066351 8155 . A . . END=8155 GT:DP:GQ:MIN_DP:PL 0/0:28:54:28:0,54,826 -20_10037292_10066351 8156 . A . . END=8156 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8157 . C . . END=8157 GT:DP:GQ:MIN_DP:PL 0/0:28:54:28:0,54,782 -20_10037292_10066351 8158 . C . . END=8158 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,836 -20_10037292_10066351 8159 . A . . END=8159 GT:DP:GQ:MIN_DP:PL 0/0:27:56:27:0,56,768 -20_10037292_10066351 8160 . T . . END=8160 GT:DP:GQ:MIN_DP:PL 0/0:27:49:27:0,49,780 -20_10037292_10066351 8161 . A . . END=8161 GT:DP:GQ:MIN_DP:PL 0/0:27:48:27:0,48,760 -20_10037292_10066351 8162 . T . . END=8163 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8164 . G . . END=8164 GT:DP:GQ:MIN_DP:PL 0/0:28:66:28:0,66,833 -20_10037292_10066351 8165 . A . . END=8165 GT:DP:GQ:MIN_DP:PL 0/0:28:50:28:0,50,793 -20_10037292_10066351 8166 . T . . END=8167 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,852 -20_10037292_10066351 8168 . T . . END=8168 GT:DP:GQ:MIN_DP:PL 0/0:26:40:26:0,40,718 -20_10037292_10066351 8169 . G . . END=8169 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8170 . G . . END=8170 GT:DP:GQ:MIN_DP:PL 0/0:27:43:27:0,43,761 -20_10037292_10066351 8171 . A . . END=8171 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,744 -20_10037292_10066351 8172 . A . . END=8172 GT:DP:GQ:MIN_DP:PL 0/0:28:9:28:0,9,692 -20_10037292_10066351 8173 . A . . END=8173 GT:DP:GQ:MIN_DP:PL 0/0:28:57:28:0,57,856 -20_10037292_10066351 8174 . G . . END=8174 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,870 -20_10037292_10066351 8175 . T . . END=8175 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,885 -20_10037292_10066351 8176 . G . . END=8176 GT:DP:GQ:MIN_DP:PL 0/0:30:32:30:0,32,810 -20_10037292_10066351 8177 . A . . END=8177 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8178 . T . . END=8178 GT:DP:GQ:MIN_DP:PL 0/0:33:38:33:0,38,893 -20_10037292_10066351 8179 . G . . END=8179 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,895 -20_10037292_10066351 8180 . G . . END=8180 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,931 -20_10037292_10066351 8181 . A . . END=8181 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,985 -20_10037292_10066351 8182 . T . . END=8182 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1018 -20_10037292_10066351 8183 . T . . END=8183 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,940 -20_10037292_10066351 8184 . T . . END=8184 GT:DP:GQ:MIN_DP:PL 0/0:33:19:33:0,19,807 -20_10037292_10066351 8185 . C . . END=8185 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,934 -20_10037292_10066351 8186 . C . . END=8186 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,993 -20_10037292_10066351 8187 . A . . END=8188 GT:DP:GQ:MIN_DP:PL 0/0:34:64:34:0,64,982 -20_10037292_10066351 8189 . T . . END=8189 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1063 -20_10037292_10066351 8190 . T . . END=8190 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1158 -20_10037292_10066351 8191 . G . . END=8191 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1114 -20_10037292_10066351 8192 . A . . END=8192 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1115 -20_10037292_10066351 8193 . T . . END=8193 GT:DP:GQ:MIN_DP:PL 0/0:38:52:38:0,52,1041 -20_10037292_10066351 8194 . T . . END=8194 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 8195 . C . . END=8195 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1156 -20_10037292_10066351 8196 . T . . END=8196 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1142 -20_10037292_10066351 8197 . G . . END=8197 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1113 -20_10037292_10066351 8198 . C . . END=8198 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1170 -20_10037292_10066351 8199 . T . . END=8200 GT:DP:GQ:MIN_DP:PL 0/0:38:73:38:0,73,1056 -20_10037292_10066351 8201 . A . . END=8204 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1009 -20_10037292_10066351 8205 . G . . END=8205 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,992 -20_10037292_10066351 8206 . T . . END=8206 GT:DP:GQ:MIN_DP:PL 0/0:38:36:38:0,36,1047 -20_10037292_10066351 8207 . C . . END=8207 GT:DP:GQ:MIN_DP:PL 0/0:39:85:39:0,85,1120 -20_10037292_10066351 8208 . C . . END=8208 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1126 -20_10037292_10066351 8209 . C . . END=8209 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1117 -20_10037292_10066351 8210 . T . . END=8210 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1226 -20_10037292_10066351 8211 . T . . END=8211 GT:DP:GQ:MIN_DP:PL 0/0:39:83:39:0,83,1161 -20_10037292_10066351 8212 . G . . END=8228 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,100,1138 -20_10037292_10066351 8229 . G . . END=8229 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1080 -20_10037292_10066351 8230 . A . . END=8233 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1530 -20_10037292_10066351 8234 . T . . END=8234 GT:DP:GQ:MIN_DP:PL 0/0:36:60:36:0,60,1038 -20_10037292_10066351 8235 . A . . END=8235 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1158 -20_10037292_10066351 8236 . G . . END=8236 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8237 . C . . END=8237 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1069 -20_10037292_10066351 8238 . A . . END=8243 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8244 . A . . END=8244 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1065 -20_10037292_10066351 8245 . C . . END=8249 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1022 -20_10037292_10066351 8250 . T . . END=8250 GT:DP:GQ:MIN_DP:PL 0/0:33:88:33:0,88,999 -20_10037292_10066351 8251 . C . . END=8251 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,993 -20_10037292_10066351 8252 . C . . END=8256 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1012 -20_10037292_10066351 8257 . G . . END=8257 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1098 -20_10037292_10066351 8258 . C . . END=8259 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 8260 . T . . END=8260 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1112 -20_10037292_10066351 8261 . C . . END=8261 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1185 -20_10037292_10066351 8262 . T . . END=8268 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,102,1530 -20_10037292_10066351 8269 . C . . END=8269 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1123 -20_10037292_10066351 8270 . C . . END=8272 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 8273 . T . . END=8273 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1171 -20_10037292_10066351 8274 . G . . END=8276 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 8277 . G . . END=8277 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1134 -20_10037292_10066351 8278 . C . . END=8279 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 8280 . A . . END=8281 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1159 -20_10037292_10066351 8282 . G . . END=8283 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1186 -20_10037292_10066351 8284 . T . . END=8284 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,1228 -20_10037292_10066351 8285 . T . . END=8285 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1148 -20_10037292_10066351 8286 . T . . END=8294 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 8295 . G . . END=8295 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1093 -20_10037292_10066351 8296 . G . . END=8297 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,101,1115 -20_10037292_10066351 8298 . C . . END=8298 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1125 -20_10037292_10066351 8299 . T . . END=8299 GT:DP:GQ:MIN_DP:PL 0/0:38:49:38:0,49,1079 -20_10037292_10066351 8300 . C . . END=8300 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,111,1665 -20_10037292_10066351 8301 . T . . END=8302 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1122 -20_10037292_10066351 8303 . A . . END=8304 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 8305 . C . . END=8305 GT:DP:GQ:MIN_DP:PL 0/0:39:67:39:0,67,1110 -20_10037292_10066351 8306 . A . . END=8306 GT:DP:GQ:MIN_DP:PL 0/0:39:75:39:0,75,1116 -20_10037292_10066351 8307 . C . . END=8307 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,103,1201 -20_10037292_10066351 8308 . C . . END=8308 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1183 -20_10037292_10066351 8309 . A . . END=8309 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 8310 . G . . END=8310 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1182 -20_10037292_10066351 8311 . C . . END=8317 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,100,1175 -20_10037292_10066351 8318 . T . . END=8318 GT:DP:GQ:MIN_DP:PL 0/0:42:94:42:0,94,1226 -20_10037292_10066351 8319 . A . . END=8325 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 8326 . G . . END=8326 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1124 -20_10037292_10066351 8327 . A . . END=8328 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8329 . T . . END=8335 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 8336 . G . . END=8336 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1092 -20_10037292_10066351 8337 . A . . END=8338 GT:DP:GQ:MIN_DP:PL 0/0:38:96:37:0,96,1122 -20_10037292_10066351 8339 . T . . END=8339 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1114 -20_10037292_10066351 8340 . T . . END=8343 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8344 . A . . END=8345 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,982 -20_10037292_10066351 8346 . A . . END=8349 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1011 -20_10037292_10066351 8350 . G C, 348.64 . BaseQRankSum=-1.608;DP=31;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=111600,31;ReadPosRankSum=-0.187 GT:AD:DP:GQ:PL:SB 0/1:16,14,0:30:99:356,0,430,405,472,877:9,7,5,9 -20_10037292_10066351 8351 . A . . END=8352 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1003 -20_10037292_10066351 8353 . T . . END=8353 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8354 . T . . END=8354 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,889 -20_10037292_10066351 8355 . C . . END=8357 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8358 . A . . END=8358 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,958 -20_10037292_10066351 8359 . A . . END=8360 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 8361 . A . . END=8361 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,1111 -20_10037292_10066351 8362 . C . . END=8363 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1208 -20_10037292_10066351 8364 . G . . END=8365 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1092 -20_10037292_10066351 8366 . A . . END=8366 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1109 -20_10037292_10066351 8367 . T . . END=8367 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1118 -20_10037292_10066351 8368 . T . . END=8373 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1084 -20_10037292_10066351 8374 . G . . END=8374 GT:DP:GQ:MIN_DP:PL 0/0:39:74:39:0,74,1095 -20_10037292_10066351 8375 . G . . END=8375 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1205 -20_10037292_10066351 8376 . G . . END=8376 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 8377 . T . . END=8377 GT:DP:GQ:MIN_DP:PL 0/0:39:89:39:0,89,1104 -20_10037292_10066351 8378 . G . . END=8378 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 8379 . G . . END=8379 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1095 -20_10037292_10066351 8380 . A . . END=8391 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,107,1152 -20_10037292_10066351 8392 . T . . END=8392 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1195 -20_10037292_10066351 8393 . G . . END=8411 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1139 -20_10037292_10066351 8412 . T . . END=8414 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 8415 . A . . END=8426 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 8427 . T . . END=8427 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,973 -20_10037292_10066351 8428 . C . . END=8431 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8432 . C . . END=8432 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1129 -20_10037292_10066351 8433 . T . . END=8435 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1159 -20_10037292_10066351 8436 . C . . END=8436 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1097 -20_10037292_10066351 8437 . T . . END=8446 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1530 -20_10037292_10066351 8447 . T . . END=8447 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1078 -20_10037292_10066351 8448 . C . . END=8449 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 8450 . C . . END=8450 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1098 -20_10037292_10066351 8451 . A . . END=8454 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8455 . T . . END=8458 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 8459 . G . . END=8459 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1035 -20_10037292_10066351 8460 . C . . END=8468 GT:DP:GQ:MIN_DP:PL 0/0:35:93:32:0,93,1018 -20_10037292_10066351 8469 . T . . END=8469 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8470 . C . . END=8472 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1098 -20_10037292_10066351 8473 . T . . END=8475 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 8476 . A . . END=8476 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1027 -20_10037292_10066351 8477 . C . . END=8479 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1039 -20_10037292_10066351 8480 . G . . END=8482 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8483 . T . . END=8484 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1037 -20_10037292_10066351 8485 . T . . END=8485 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8486 . A . . END=8491 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8492 . T . . END=8492 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1010 -20_10037292_10066351 8493 . G . . END=8495 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8496 . A . . END=8497 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,996 -20_10037292_10066351 8498 . C . . END=8498 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,962 -20_10037292_10066351 8499 . T . . END=8499 GT:DP:GQ:MIN_DP:PL 0/0:32:58:32:0,58,904 -20_10037292_10066351 8500 . C . . END=8500 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,901 -20_10037292_10066351 8501 . C . . END=8503 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8504 . C . . END=8508 GT:DP:GQ:MIN_DP:PL 0/0:34:81:32:0,81,1215 -20_10037292_10066351 8509 . G . . END=8511 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,936 -20_10037292_10066351 8512 . A . . END=8513 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8514 . A . . END=8514 GT:DP:GQ:MIN_DP:PL 0/0:30:62:30:0,62,808 -20_10037292_10066351 8515 . A . . END=8519 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 8520 . G . . END=8520 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,913 -20_10037292_10066351 8521 . C . . END=8521 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 8522 . A . . END=8529 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1014 -20_10037292_10066351 8530 . C . . END=8530 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,1017 -20_10037292_10066351 8531 . C . . END=8531 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1077 -20_10037292_10066351 8532 . A . . END=8532 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1093 -20_10037292_10066351 8533 . C . . END=8536 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,111,1179 -20_10037292_10066351 8537 . A . . END=8537 GT:DP:GQ:MIN_DP:PL 0/0:40:94:40:0,94,1186 -20_10037292_10066351 8538 . A . . END=8542 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,102,1184 -20_10037292_10066351 8543 . C . . END=8543 GT:DP:GQ:MIN_DP:PL 0/0:42:76:42:0,76,1186 -20_10037292_10066351 8544 . A . . END=8576 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1160 -20_10037292_10066351 8577 . G . . END=8577 GT:DP:GQ:MIN_DP:PL 0/0:38:95:38:0,95,1108 -20_10037292_10066351 8578 . T . . END=8582 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 8583 . T . . END=8583 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1108 -20_10037292_10066351 8584 . T . . END=8584 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 8585 . T . . END=8585 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1034 -20_10037292_10066351 8586 . C . . END=8588 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1041 -20_10037292_10066351 8589 . A . . END=8597 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,100,1141 -20_10037292_10066351 8598 . T . . END=8598 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1217 -20_10037292_10066351 8599 . G . . END=8644 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,99,1152 -20_10037292_10066351 8645 . T . . END=8645 GT:DP:GQ:MIN_DP:PL 0/0:44:97:44:0,97,1160 -20_10037292_10066351 8646 . C . . END=8670 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,106,1261 -20_10037292_10066351 8671 . A . . END=8671 GT:DP:GQ:MIN_DP:PL 0/0:46:94:46:0,94,1264 -20_10037292_10066351 8672 . C . . END=8710 GT:DP:GQ:MIN_DP:PL 0/0:45:99:41:0,102,1234 -20_10037292_10066351 8711 . C . . END=8711 GT:DP:GQ:MIN_DP:PL 0/0:45:98:45:0,98,1210 -20_10037292_10066351 8712 . C . . END=8719 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,120,1800 -20_10037292_10066351 8720 . C . . END=8720 GT:DP:GQ:MIN_DP:PL 0/0:47:95:47:0,95,1205 -20_10037292_10066351 8721 . A . . END=8758 GT:DP:GQ:MIN_DP:PL 0/0:50:99:47:0,101,1253 -20_10037292_10066351 8759 . C . . END=8759 GT:DP:GQ:MIN_DP:PL 0/0:51:98:51:0,98,1318 -20_10037292_10066351 8760 . T . . END=8772 GT:DP:GQ:MIN_DP:PL 0/0:50:99:48:0,112,1331 -20_10037292_10066351 8773 . G . . END=8773 GT:DP:GQ:MIN_DP:PL 0/0:47:90:47:0,90,1345 -20_10037292_10066351 8774 . G . . END=8798 GT:DP:GQ:MIN_DP:PL 0/0:47:99:46:0,100,1267 -20_10037292_10066351 8799 . T . . END=8799 GT:DP:GQ:MIN_DP:PL 0/0:46:91:46:0,91,1314 -20_10037292_10066351 8800 . C . . END=8816 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,107,1273 -20_10037292_10066351 8817 . T . . END=8817 GT:DP:GQ:MIN_DP:PL 0/0:43:9:43:0,9,868 -20_10037292_10066351 8818 . T . . END=8818 GT:DP:GQ:MIN_DP:PL 0/0:43:69:43:0,69,1016 -20_10037292_10066351 8819 . A . . END=8823 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,103,1274 -20_10037292_10066351 8824 . T . . END=8824 GT:DP:GQ:MIN_DP:PL 0/0:41:43:41:0,43,1059 -20_10037292_10066351 8825 . G . . END=8825 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,114,1710 -20_10037292_10066351 8826 . C . . END=8826 GT:DP:GQ:MIN_DP:PL 0/0:42:80:42:0,80,1084 -20_10037292_10066351 8827 . T . . END=8827 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1150 -20_10037292_10066351 8828 . G . . END=8834 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,105,1575 -20_10037292_10066351 8835 . C . . END=8835 GT:DP:GQ:MIN_DP:PL 0/0:43:66:43:0,66,1018 -20_10037292_10066351 8836 . A . . END=8845 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1238 -20_10037292_10066351 8846 . G . . END=8846 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1131 -20_10037292_10066351 8847 . G . . END=8852 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1077 -20_10037292_10066351 8853 . G . . END=8853 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1079 -20_10037292_10066351 8854 . A . . END=8859 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1103 -20_10037292_10066351 8860 . A . . END=8862 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 8863 . G . . END=8863 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,988 -20_10037292_10066351 8864 . G . . END=8864 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,955 -20_10037292_10066351 8865 . G . . END=8865 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1170 -20_10037292_10066351 8866 . A . . END=8866 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1215 -20_10037292_10066351 8867 . A . . END=8870 GT:DP:GQ:MIN_DP:PL 0/0:37:70:35:0,70,1040 -20_10037292_10066351 8871 . G . . END=8871 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,952 -20_10037292_10066351 8872 . A . . END=8872 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1019 -20_10037292_10066351 8873 . A . . END=8873 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 8874 . A . . END=8875 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1009 -20_10037292_10066351 8876 . A . . END=8876 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1170 -20_10037292_10066351 8877 . A . . END=8878 GT:DP:GQ:MIN_DP:PL 0/0:35:81:34:0,81,944 -20_10037292_10066351 8879 . A . . END=8880 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 8881 . A . . END=8882 GT:DP:GQ:MIN_DP:PL 0/0:34:81:34:0,81,1215 -20_10037292_10066351 8883 . A . . END=8883 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,1170 -20_10037292_10066351 8884 . G . . END=8884 GT:DP:GQ:MIN_DP:PL 0/0:28:0:28:0,0,701 -20_10037292_10066351 8885 . A . . END=8885 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,929 -20_10037292_10066351 8886 . AAGAAAGAAAG A, 790.03 . DP=25;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=90000,25 GT:AD:DP:GQ:PL:SB 1/1:0,18,0:18:55:804,55,0,804,55,804:0,0,15,3 -20_10037292_10066351 8897 . A . . END=8897 GT:DP:GQ:MIN_DP:PL 0/0:33:29:33:0,29,882 -20_10037292_10066351 8898 . G . . END=8898 GT:DP:GQ:MIN_DP:PL 0/0:30:0:30:0,0,664 -20_10037292_10066351 8899 . A . . END=8899 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,870 -20_10037292_10066351 8900 . A . . END=8900 GT:DP:GQ:MIN_DP:PL 0/0:29:53:29:0,53,859 -20_10037292_10066351 8901 . A . . END=8901 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 8902 . G . . END=8902 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,742 -20_10037292_10066351 8903 . A . . END=8903 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,1080 -20_10037292_10066351 8904 . A . . END=8904 GT:DP:GQ:MIN_DP:PL 0/0:30:0:30:0,0,653 -20_10037292_10066351 8905 . A . . END=8905 GT:DP:GQ:MIN_DP:PL 0/0:30:55:30:0,55,917 -20_10037292_10066351 8906 . G . . END=8906 GT:DP:GQ:MIN_DP:PL 0/0:30:0:30:0,0,592 -20_10037292_10066351 8907 . A . . END=8907 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8908 . G . . END=8908 GT:DP:GQ:MIN_DP:PL 0/0:29:56:29:0,56,775 -20_10037292_10066351 8909 . A . . END=8911 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 8912 . G . . END=8912 GT:DP:GQ:MIN_DP:PL 0/0:31:45:31:0,45,778 -20_10037292_10066351 8913 . A . . END=8913 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8914 . G . . END=8914 GT:DP:GQ:MIN_DP:PL 0/0:32:39:32:0,39,789 -20_10037292_10066351 8915 . A . . END=8915 GT:DP:GQ:MIN_DP:PL 0/0:32:55:32:0,55,861 -20_10037292_10066351 8916 . A . . END=8916 GT:DP:GQ:MIN_DP:PL 0/0:33:73:33:0,73,936 -20_10037292_10066351 8917 . A . . END=8917 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8918 . G . . END=8918 GT:DP:GQ:MIN_DP:PL 0/0:32:41:32:0,41,862 -20_10037292_10066351 8919 . A . . END=8919 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,852 -20_10037292_10066351 8920 . A . . END=8921 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8922 . G . . END=8922 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,813 -20_10037292_10066351 8923 . A . . END=8923 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8924 . G . . END=8924 GT:DP:GQ:MIN_DP:PL 0/0:32:24:32:0,24,782 -20_10037292_10066351 8925 . G . . END=8925 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,854 -20_10037292_10066351 8926 . A . . END=8927 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8928 . A . . END=8928 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,978 -20_10037292_10066351 8929 . G . . END=8929 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,916 -20_10037292_10066351 8930 . A . . END=8930 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,971 -20_10037292_10066351 8931 . G . . END=8931 GT:DP:GQ:MIN_DP:PL 0/0:34:55:34:0,55,861 -20_10037292_10066351 8932 . A . . END=8932 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 8933 . G . . END=8933 GT:DP:GQ:MIN_DP:PL 0/0:34:55:34:0,55,871 -20_10037292_10066351 8934 . A . . END=8934 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8935 . A . . END=8935 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,929 -20_10037292_10066351 8936 . A . . END=8936 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8937 . G . . END=8937 GT:DP:GQ:MIN_DP:PL 0/0:34:41:34:0,41,873 -20_10037292_10066351 8938 . A . . END=8942 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8943 . G . . END=8943 GT:DP:GQ:MIN_DP:PL 0/0:34:56:34:0,56,859 -20_10037292_10066351 8944 . A . . END=8944 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 8945 . G . . END=8945 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,999 -20_10037292_10066351 8946 . A . . END=8947 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8948 . G . . END=8948 GT:DP:GQ:MIN_DP:PL 0/0:35:70:35:0,70,915 -20_10037292_10066351 8949 . G . . END=8949 GT:DP:GQ:MIN_DP:PL 0/0:35:57:35:0,57,843 -20_10037292_10066351 8950 . A . . END=8950 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 8951 . A . . END=8951 GT:DP:GQ:MIN_DP:PL 0/0:33:77:33:0,77,925 -20_10037292_10066351 8952 . A . . END=8952 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 8953 . G . . END=8953 GT:DP:GQ:MIN_DP:PL 0/0:33:59:33:0,59,854 -20_10037292_10066351 8954 . A . . END=8954 GT:DP:GQ:MIN_DP:PL 0/0:34:83:34:0,83,996 -20_10037292_10066351 8955 . G . . END=8955 GT:DP:GQ:MIN_DP:PL 0/0:34:65:34:0,65,855 -20_10037292_10066351 8956 . A . . END=8958 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8959 . G . . END=8959 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,870 -20_10037292_10066351 8960 . A . . END=8963 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,893 -20_10037292_10066351 8964 . A . . END=8964 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8965 . G . . END=8965 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,921 -20_10037292_10066351 8966 . A . . END=8966 GT:DP:GQ:MIN_DP:PL 0/0:33:79:33:0,79,885 -20_10037292_10066351 8967 . A . . END=8967 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8968 . G . . END=8969 GT:DP:GQ:MIN_DP:PL 0/0:31:75:30:0,75,807 -20_10037292_10066351 8970 . A . . END=8975 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 8976 . A . . END=8977 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,807 -20_10037292_10066351 8978 . A . . END=8983 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,904 -20_10037292_10066351 8984 . A . . END=8986 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 8987 . G . . END=8987 GT:DP:GQ:MIN_DP:PL 0/0:32:65:32:0,65,811 -20_10037292_10066351 8988 . A . . END=8988 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,954 -20_10037292_10066351 8989 . G . . END=8989 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,832 -20_10037292_10066351 8990 . A . . END=8992 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8993 . G . . END=8994 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8995 . G . . END=8995 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,964 -20_10037292_10066351 8996 . A . . END=8996 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8997 . G . . END=8998 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,927 -20_10037292_10066351 8999 . G . . END=8999 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,935 -20_10037292_10066351 9000 . A . . END=9001 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9002 . A . . END=9011 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1019 -20_10037292_10066351 9012 . G . . END=9012 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 9013 . A . . END=9013 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 9014 . A . . END=9014 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1063 -20_10037292_10066351 9015 . G . . END=9018 GT:DP:GQ:MIN_DP:PL 0/0:38:90:37:0,90,991 -20_10037292_10066351 9019 . G . . END=9019 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,933 -20_10037292_10066351 9020 . A . . END=9022 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1066 -20_10037292_10066351 9023 . A . . END=9023 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,965 -20_10037292_10066351 9024 . A . . END=9024 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9025 . T . . END=9025 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,801 -20_10037292_10066351 9026 . G . . END=9030 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,105,1575 -20_10037292_10066351 9031 . G . . END=9031 GT:DP:GQ:MIN_DP:PL 0/0:39:66:39:0,66,992 -20_10037292_10066351 9032 . A . . END=9032 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 9033 . G . . END=9033 GT:DP:GQ:MIN_DP:PL 0/0:40:59:40:0,59,1001 -20_10037292_10066351 9034 . G . . END=9034 GT:DP:GQ:MIN_DP:PL 0/0:40:55:40:0,55,938 -20_10037292_10066351 9035 . A . . END=9036 GT:DP:GQ:MIN_DP:PL 0/0:40:84:39:0,84,1028 -20_10037292_10066351 9037 . G . . END=9037 GT:DP:GQ:MIN_DP:PL 0/0:38:13:38:0,13,819 -20_10037292_10066351 9038 . G . . END=9038 GT:DP:GQ:MIN_DP:PL 0/0:36:66:36:0,66,886 -20_10037292_10066351 9039 . A . . END=9044 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,101,1102 -20_10037292_10066351 9045 . G . . END=9045 GT:DP:GQ:MIN_DP:PL 0/0:38:80:38:0,80,1032 -20_10037292_10066351 9046 . A . . END=9046 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 9047 . G . . END=9047 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,992 -20_10037292_10066351 9048 . A . . END=9048 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9049 . C . . END=9049 GT:DP:GQ:MIN_DP:PL 0/0:35:75:35:0,75,843 -20_10037292_10066351 9050 . A . . END=9056 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 9057 . A . . END=9057 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 9058 . A . . END=9058 GT:DP:GQ:MIN_DP:PL 0/0:36:64:36:0,64,986 -20_10037292_10066351 9059 . G . . END=9060 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 9061 . A . . END=9070 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,1260 -20_10037292_10066351 9071 . A . . END=9071 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9072 . G . . END=9072 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1060 -20_10037292_10066351 9073 . A . . END=9073 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9074 . A . . END=9074 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 9075 . A . . END=9077 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1395 -20_10037292_10066351 9078 . A . . END=9079 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,986 -20_10037292_10066351 9080 . A . . END=9081 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9082 . A . . END=9082 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,984 -20_10037292_10066351 9083 . G . . END=9085 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 9086 . G . . END=9086 GT:DP:GQ:MIN_DP:PL 0/0:33:80:33:0,80,954 -20_10037292_10066351 9087 . A . . END=9087 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,899 -20_10037292_10066351 9088 . A . . END=9088 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,992 -20_10037292_10066351 9089 . G . . END=9096 GT:DP:GQ:MIN_DP:PL 0/0:35:90:32:0,90,1350 -20_10037292_10066351 9097 . A . . END=9097 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,971 -20_10037292_10066351 9098 . G . . END=9099 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9100 . A . . END=9100 GT:DP:GQ:MIN_DP:PL 0/0:33:73:33:0,73,999 -20_10037292_10066351 9101 . A . . END=9103 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 9104 . A . . END=9107 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,943 -20_10037292_10066351 9108 . A . . END=9110 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9111 . A . . END=9111 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,972 -20_10037292_10066351 9112 . A . . END=9117 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9118 . A . . END=9133 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1099 -20_10037292_10066351 9134 . A . . END=9134 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1061 -20_10037292_10066351 9135 . A . . END=9135 GT:DP:GQ:MIN_DP:PL 0/0:36:82:36:0,82,1064 -20_10037292_10066351 9136 . A . . END=9136 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9137 . C . . END=9137 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1079 -20_10037292_10066351 9138 . C . . END=9140 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9141 . A . . END=9141 GT:DP:GQ:MIN_DP:PL 0/0:37:85:37:0,85,1117 -20_10037292_10066351 9142 . A . . END=9142 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1124 -20_10037292_10066351 9143 . A . . END=9143 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9144 . A . . END=9144 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1143 -20_10037292_10066351 9145 . G . . END=9152 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1142 -20_10037292_10066351 9153 . T . . END=9153 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1295 -20_10037292_10066351 9154 . A . . END=9176 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,102,1254 -20_10037292_10066351 9177 . T . . END=9177 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1212 -20_10037292_10066351 9178 . G . . END=9180 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,107,1119 -20_10037292_10066351 9181 . G . . END=9181 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1056 -20_10037292_10066351 9182 . G . . END=9184 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1197 -20_10037292_10066351 9185 . T . . END=9185 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1152 -20_10037292_10066351 9186 . T . . END=9186 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1209 -20_10037292_10066351 9187 . T . . END=9187 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1113 -20_10037292_10066351 9188 . C . . END=9193 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,105,1208 -20_10037292_10066351 9194 . A . . END=9194 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1134 -20_10037292_10066351 9195 . C . . END=9201 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,102,1314 -20_10037292_10066351 9202 . T . . END=9202 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1233 -20_10037292_10066351 9203 . C . . END=9246 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,114,1272 -20_10037292_10066351 9247 . T . . END=9247 GT:DP:GQ:MIN_DP:PL 0/0:44:90:44:0,90,1239 -20_10037292_10066351 9248 . T . . END=9263 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,117,1755 -20_10037292_10066351 9264 . A . . END=9264 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1293 -20_10037292_10066351 9265 . A . . END=9280 GT:DP:GQ:MIN_DP:PL 0/0:44:99:41:0,106,1208 -20_10037292_10066351 9281 . T . . END=9281 GT:DP:GQ:MIN_DP:PL 0/0:45:89:45:0,89,1396 -20_10037292_10066351 9282 . G . . END=9301 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,99,1485 -20_10037292_10066351 9302 . A . . END=9306 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 9307 . A . . END=9309 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 9310 . C . . END=9314 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1141 -20_10037292_10066351 9315 . G . . END=9360 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,102,1243 -20_10037292_10066351 9361 . G . . END=9361 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1076 -20_10037292_10066351 9362 . C . . END=9369 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,105,1575 -20_10037292_10066351 9370 . A . . END=9370 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1042 -20_10037292_10066351 9371 . C . . END=9374 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 9375 . A . . END=9375 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1118 -20_10037292_10066351 9376 . C . . END=9376 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9377 . A . . END=9382 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1117 -20_10037292_10066351 9383 . C . . END=9385 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9386 . A . . END=9386 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1091 -20_10037292_10066351 9387 . T . . END=9400 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1158 -20_10037292_10066351 9401 . T . . END=9401 GT:DP:GQ:MIN_DP:PL 0/0:36:73:36:0,73,1066 -20_10037292_10066351 9402 . C . . END=9408 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1143 -20_10037292_10066351 9409 . C . . END=9409 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1193 -20_10037292_10066351 9410 . C . . END=9412 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,111,1665 -20_10037292_10066351 9413 . C . . END=9413 GT:DP:GQ:MIN_DP:PL 0/0:42:94:42:0,94,1240 -20_10037292_10066351 9414 . C . . END=9463 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,104,1316 -20_10037292_10066351 9464 . A . . END=9464 GT:DP:GQ:MIN_DP:PL 0/0:42:79:42:0,79,1237 -20_10037292_10066351 9465 . A . . END=9468 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 9469 . T . . END=9469 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1174 -20_10037292_10066351 9470 . C . . END=9478 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1485 -20_10037292_10066351 9479 . A . . END=9480 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 9481 . G . . END=9484 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 9485 . A . . END=9486 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1037 -20_10037292_10066351 9487 . C . . END=9492 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 9493 . G . . END=9493 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1162 -20_10037292_10066351 9494 . A . . END=9496 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9497 . T . . END=9497 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1105 -20_10037292_10066351 9498 . C . . END=9513 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1169 -20_10037292_10066351 9514 . C . . END=9514 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1203 -20_10037292_10066351 9515 . C . . END=9533 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,105,1101 -20_10037292_10066351 9534 . A . . END=9534 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,960 -20_10037292_10066351 9535 . A . . END=9535 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9536 . T C, 936.06 . DP=32;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=115200,32 GT:AD:DP:GQ:PL:SB 1/1:0,32,0:32:95:950,95,0,950,95,950:0,0,16,16 -20_10037292_10066351 9537 . T . . END=9537 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,993 -20_10037292_10066351 9538 . C . . END=9538 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9539 . A . . END=9540 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,974 -20_10037292_10066351 9541 . C . . END=9544 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 9545 . A . . END=9545 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1085 -20_10037292_10066351 9546 . T . . END=9546 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1088 -20_10037292_10066351 9547 . T . . END=9554 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 9555 . A . . END=9565 GT:DP:GQ:MIN_DP:PL 0/0:38:90:34:0,90,1110 -20_10037292_10066351 9566 . T . . END=9568 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 9569 . C . . END=9569 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,899 -20_10037292_10066351 9570 . T . . END=9573 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,900 -20_10037292_10066351 9574 . C . . END=9574 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 9575 . C . . END=9575 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1076 -20_10037292_10066351 9576 . T . . END=9588 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 9589 . A . . END=9589 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,952 -20_10037292_10066351 9590 . C . . END=9597 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 9598 . G . . END=9598 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,865 -20_10037292_10066351 9599 . C . . END=9600 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 9601 . G . . END=9601 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,868 -20_10037292_10066351 9602 . T . . END=9665 GT:DP:GQ:MIN_DP:PL 0/0:43:99:37:0,100,1177 -20_10037292_10066351 9666 . T . . END=9666 GT:DP:GQ:MIN_DP:PL 0/0:50:88:50:0,88,1434 -20_10037292_10066351 9667 . T . . END=9848 GT:DP:GQ:MIN_DP:PL 0/0:57:99:49:0,110,1475 -20_10037292_10066351 9849 . A . . END=9849 GT:DP:GQ:MIN_DP:PL 0/0:54:78:54:0,78,1253 -20_10037292_10066351 9850 . C . . END=9859 GT:DP:GQ:MIN_DP:PL 0/0:50:99:50:0,103,1432 -20_10037292_10066351 12912 . G . . END=12915 GT:DP:GQ:MIN_DP:PL 0/0:29:75:27:0,75,1125 -20_10037292_10066351 12916 . A . . END=12919 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 12920 . A . . END=12920 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 12921 . G . . END=12921 GT:DP:GQ:MIN_DP:PL 0/0:28:66:28:0,66,844 -20_10037292_10066351 12922 . A . . END=12927 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 -20_10037292_10066351 12928 . A . . END=12934 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 12935 . C . . END=12939 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,875 -20_10037292_10066351 12940 . A . . END=12947 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1530 -20_10037292_10066351 12948 . G . . END=12948 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,1112 -20_10037292_10066351 12949 . G . . END=12956 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 12957 . A . . END=12957 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,990 -20_10037292_10066351 12958 . A . . END=12966 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 12967 . C . . END=12976 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1350 -20_10037292_10066351 12977 . C . . END=12977 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,835 -20_10037292_10066351 12978 . A . . END=12981 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,952 -20_10037292_10066351 12982 . T . . END=12982 GT:DP:GQ:MIN_DP:PL 0/0:30:50:30:0,50,808 -20_10037292_10066351 12983 . T . . END=12986 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,886 -20_10037292_10066351 12987 . G . . END=12987 GT:DP:GQ:MIN_DP:PL 0/0:30:70:30:0,70,861 -20_10037292_10066351 12988 . A . . END=12992 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,967 -20_10037292_10066351 12993 . G . . END=12994 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 12995 . C . . END=12997 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 12998 . G . . END=12999 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 13000 . C . . END=13000 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,971 -20_10037292_10066351 13001 . C . . END=13002 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13003 . G . . END=13006 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 13007 . T . . END=13011 GT:DP:GQ:MIN_DP:PL 0/0:30:80:28:0,80,804 -20_10037292_10066351 13012 . G . . END=13012 GT:DP:GQ:MIN_DP:PL 0/0:30:61:30:0,61,937 -20_10037292_10066351 13013 . A . . END=13015 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 13016 . T . . END=13023 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,817 -20_10037292_10066351 13024 . A . . END=13024 GT:DP:GQ:MIN_DP:PL 0/0:31:82:31:0,82,915 -20_10037292_10066351 13025 . A . . END=13027 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,954 -20_10037292_10066351 13028 . G . . END=13028 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13029 . T . . END=13029 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,799 -20_10037292_10066351 13030 . A . . END=13033 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 13034 . A . . END=13034 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13035 . G . . END=13035 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13036 . T . . END=13037 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 13038 . T . . END=13038 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,969 -20_10037292_10066351 13039 . G . . END=13042 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13043 . T . . END=13043 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,992 -20_10037292_10066351 13044 . T . . END=13047 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,959 -20_10037292_10066351 13048 . T . . END=13062 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1011 -20_10037292_10066351 13063 . T . . END=13063 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1061 -20_10037292_10066351 13064 . T . . END=13064 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1049 -20_10037292_10066351 13065 . T . . END=13068 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1087 -20_10037292_10066351 13069 . C . . END=13072 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1102 -20_10037292_10066351 13073 . G . . END=13073 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 13074 . C . . END=13074 GT:DP:GQ:MIN_DP:PL 0/0:36:87:36:0,87,1305 -20_10037292_10066351 13075 . T . . END=13077 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 13078 . T . . END=13080 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 13081 . C . . END=13082 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 13083 . T . . END=13083 GT:DP:GQ:MIN_DP:PL 0/0:35:81:35:0,81,929 -20_10037292_10066351 13084 . C . . END=13084 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 13085 . T . . END=13085 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 13086 . C . . END=13088 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1395 -20_10037292_10066351 13089 . A . . END=13089 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1050 -20_10037292_10066351 13090 . A . . END=13092 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1062 -20_10037292_10066351 13093 . G . . END=13094 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 13095 . T . . END=13095 GT:DP:GQ:MIN_DP:PL 0/0:34:63:34:0,63,942 -20_10037292_10066351 13096 . T . . END=13098 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1047 -20_10037292_10066351 13099 . A . . END=13102 GT:DP:GQ:MIN_DP:PL 0/0:35:93:33:0,93,1395 -20_10037292_10066351 13103 . C . . END=13103 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1050 -20_10037292_10066351 13104 . A . . END=13104 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13105 . C . . END=13125 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1127 -20_10037292_10066351 13126 . A . . END=13126 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1081 -20_10037292_10066351 13127 . A . . END=13127 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,100,1131 -20_10037292_10066351 13128 . T . . END=13128 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1135 -20_10037292_10066351 13129 . T . . END=13159 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,107,1215 -20_10037292_10066351 13160 . T . . END=13160 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1223 -20_10037292_10066351 13161 . T . . END=13168 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,106,1237 -20_10037292_10066351 13169 . G . . END=13170 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1217 -20_10037292_10066351 13171 . C . . END=13189 GT:DP:GQ:MIN_DP:PL 0/0:46:99:43:0,99,1275 -20_10037292_10066351 13190 . A . . END=13190 GT:DP:GQ:MIN_DP:PL 0/0:45:91:45:0,91,1329 -20_10037292_10066351 13191 . G . . END=13209 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,100,1211 -20_10037292_10066351 13210 . A . . END=13210 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1107 -20_10037292_10066351 13211 . G . . END=13374 GT:DP:GQ:MIN_DP:PL 0/0:44:99:37:0,99,1159 -20_10037292_10066351 13375 . C T, 725.64 . BaseQRankSum=0.171;DP=58;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=208800,58;ReadPosRankSum=0.415 GT:AD:DP:GQ:PL:SB 0/1:28,29,0:57:99:733,0,679,816,765,1581:14,14,9,20 -20_10037292_10066351 13376 . C . . END=13438 GT:DP:GQ:MIN_DP:PL 0/0:55:99:47:0,111,1631 -20_10037292_10066351 13439 . G . . END=13439 GT:DP:GQ:MIN_DP:PL 0/0:47:90:47:0,90,1325 -20_10037292_10066351 13440 . T . . END=13455 GT:DP:GQ:MIN_DP:PL 0/0:46:99:44:0,102,1278 -20_10037292_10066351 13456 . C . . END=13456 GT:DP:GQ:MIN_DP:PL 0/0:46:94:46:0,94,1305 -20_10037292_10066351 13457 . T . . END=13487 GT:DP:GQ:MIN_DP:PL 0/0:47:99:40:0,107,1330 -20_10037292_10066351 13488 . A . . END=13488 GT:DP:GQ:MIN_DP:PL 0/0:39:72:39:0,72,1128 -20_10037292_10066351 13489 . C . . END=13489 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 13490 . A . . END=13490 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,1203 -20_10037292_10066351 13491 . G . . END=13535 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,99,1231 -20_10037292_10066351 13536 . T C, 583.64 . BaseQRankSum=1.634;DP=44;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=158400,44;ReadPosRankSum=-0.200 GT:AD:DP:GQ:PL:SB 0/1:21,23,0:44:99:591,0,526,654,594,1248:9,12,12,11 -20_10037292_10066351 13537 . T . . END=13687 GT:DP:GQ:MIN_DP:PL 0/0:49:99:38:0,103,1209 -20_10037292_10066351 13688 . A . . END=13688 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1191 -20_10037292_10066351 13689 . T . . END=13691 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 13692 . T . . END=13692 GT:DP:GQ:MIN_DP:PL 0/0:39:89:39:0,89,1224 -20_10037292_10066351 13693 . C . . END=13745 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,100,1220 -20_10037292_10066351 13746 . A . . END=13746 GT:DP:GQ:MIN_DP:PL 0/0:48:82:48:0,82,1344 -20_10037292_10066351 13747 . G . . END=13875 GT:DP:GQ:MIN_DP:PL 0/0:48:99:42:0,101,1231 -20_10037292_10066351 13876 . A . . END=13876 GT:DP:GQ:MIN_DP:PL 0/0:40:73:40:0,73,1107 -20_10037292_10066351 13877 . A . . END=13881 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,116,1281 -20_10037292_10066351 13882 . C . . END=13882 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1274 -20_10037292_10066351 13883 . C . . END=13893 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,101,1231 -20_10037292_10066351 13894 . T . . END=13894 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1440 -20_10037292_10066351 13895 . A . . END=13895 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1186 -20_10037292_10066351 13896 . A . . END=13897 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13898 . T . . END=13898 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1055 -20_10037292_10066351 13899 . T . . END=13899 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1008 -20_10037292_10066351 13900 . A . . END=13900 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13901 . T . . END=13915 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,1034 -20_10037292_10066351 13916 . T . . END=13916 GT:DP:GQ:MIN_DP:PL 0/0:42:91:42:0,91,1137 -20_10037292_10066351 13917 . A . . END=13918 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,100,1176 -20_10037292_10066351 13919 . T . . END=13919 GT:DP:GQ:MIN_DP:PL 0/0:42:94:42:0,94,1163 -20_10037292_10066351 13920 . T . . END=13941 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,103,1099 -20_10037292_10066351 13942 . T . . END=13942 GT:DP:GQ:MIN_DP:PL 0/0:42:95:42:0,95,1134 -20_10037292_10066351 13943 . A . . END=13981 GT:DP:GQ:MIN_DP:PL 0/0:45:99:41:0,102,1152 -20_10037292_10066351 13982 . G . . END=13982 GT:DP:GQ:MIN_DP:PL 0/0:45:94:45:0,94,1300 -20_10037292_10066351 13983 . A . . END=13992 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,113,1242 -20_10037292_10066351 13993 . A . . END=13993 GT:DP:GQ:MIN_DP:PL 0/0:43:93:43:0,93,1200 -20_10037292_10066351 13994 . T . . END=14022 GT:DP:GQ:MIN_DP:PL 0/0:44:99:38:0,105,1172 -20_10037292_10066351 14023 . C . . END=14023 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1103 -20_10037292_10066351 14024 . A . . END=14037 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,102,1121 -20_10037292_10066351 14038 . G . . END=14038 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1166 -20_10037292_10066351 14039 . T . . END=14042 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,101,1109 -20_10037292_10066351 14043 . A . . END=14043 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1105 -20_10037292_10066351 14044 . A . . END=14051 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,108,1620 -20_10037292_10066351 14052 . G . . END=14063 GT:DP:GQ:MIN_DP:PL 0/0:38:96:36:0,96,1440 -20_10037292_10066351 14064 . G . . END=14064 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 14065 . T . . END=14065 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,859 -20_10037292_10066351 14066 . G . . END=14066 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 14067 . C . . END=14075 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 14076 . T . . END=14076 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,986 -20_10037292_10066351 14077 . T . . END=14079 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 14080 . A . . END=14081 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1009 -20_10037292_10066351 14082 . C . . END=14084 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 14085 . C . . END=14085 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1104 -20_10037292_10066351 14086 . C . . END=14086 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 14087 . A . . END=14097 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 14098 . G . . END=14099 GT:DP:GQ:MIN_DP:PL 0/0:33:80:32:0,80,872 -20_10037292_10066351 14100 . A . . END=14101 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1011 -20_10037292_10066351 14102 . T . . END=14102 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,929 -20_10037292_10066351 14103 . C . . END=14103 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 14104 . A . . END=14104 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,971 -20_10037292_10066351 14105 . C . . END=14107 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 14108 . A . . END=14108 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 14109 . C . . END=14109 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,995 -20_10037292_10066351 14110 . T . . END=14112 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 14113 . A . . END=14118 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1043 -20_10037292_10066351 14119 . T . . END=14119 GT:DP:GQ:MIN_DP:PL 0/0:36:85:36:0,85,1054 -20_10037292_10066351 14120 . C . . END=14123 GT:DP:GQ:MIN_DP:PL 0/0:36:93:34:0,93,1395 -20_10037292_10066351 14124 . C . . END=14124 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1014 -20_10037292_10066351 14125 . A . . END=14125 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,1057 -20_10037292_10066351 14126 . G . . END=14126 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1037 -20_10037292_10066351 14127 . C . . END=14127 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,889 -20_10037292_10066351 14128 . G . . END=14130 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,102,1006 -20_10037292_10066351 14131 . C . . END=14131 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,991 -20_10037292_10066351 14132 . G . . END=14139 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,104,1190 -20_10037292_10066351 14140 . A . . END=14140 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1163 -20_10037292_10066351 14141 . C . . END=14155 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,100,1070 -20_10037292_10066351 14156 . T C, 250.64 . BaseQRankSum=3.197;DP=38;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=136800,38;ReadPosRankSum=1.134 GT:AD:DP:GQ:PL:SB 0/1:25,11,0:36:99:258,0,676,333,709,1042:16,9,4,7 -20_10037292_10066351 14157 . T . . END=14170 GT:DP:GQ:MIN_DP:PL 0/0:44:99:40:0,105,1282 -20_10037292_10066351 14171 . A . . END=14171 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1214 -20_10037292_10066351 14172 . C . . END=14192 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,104,1294 -20_10037292_10066351 14193 . T . . END=14193 GT:DP:GQ:MIN_DP:PL 0/0:46:92:46:0,92,1310 -20_10037292_10066351 14194 . C . . END=14268 GT:DP:GQ:MIN_DP:PL 0/0:41:99:35:0,99,1065 -20_10037292_10066351 14269 . C . . END=14272 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1092 -20_10037292_10066351 14273 . A . . END=14277 GT:DP:GQ:MIN_DP:PL 0/0:36:84:35:0,84,1260 -20_10037292_10066351 14278 . A . . END=14279 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 14280 . C . . END=14324 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,1011 -20_10037292_10066351 14325 . T . . END=14331 GT:DP:GQ:MIN_DP:PL 0/0:37:92:35:0,92,1076 -20_10037292_10066351 14332 . C . . END=14332 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1040 -20_10037292_10066351 14333 . T . . END=14335 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 14336 . G . . END=14336 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1026 -20_10037292_10066351 14337 . A . . END=14338 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 14339 . G . . END=14344 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 14345 . A . . END=14348 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 14349 . T . . END=14351 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 14352 . G . . END=14352 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1064 -20_10037292_10066351 14353 . T . . END=14376 GT:DP:GQ:MIN_DP:PL 0/0:40:99:35:0,99,1159 -20_10037292_10066351 14377 . C . . END=14377 GT:DP:GQ:MIN_DP:PL 0/0:45:92:45:0,92,1330 -20_10037292_10066351 14378 . C . . END=14402 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,110,1227 -20_10037292_10066351 14403 . G A, 145.64 . BaseQRankSum=2.632;DP=42;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=151200,42;ReadPosRankSum=0.252 GT:AD:DP:GQ:PL:SB 0/1:32,9,0:41:99:153,0,821,249,848,1097:15,17,5,4 -20_10037292_10066351 14404 . T . . END=14450 GT:DP:GQ:MIN_DP:PL 0/0:43:99:37:0,99,1183 -20_10037292_10066351 14451 . T . . END=14454 GT:DP:GQ:MIN_DP:PL 0/0:38:90:37:0,90,1350 -20_10037292_10066351 14455 . G . . END=14457 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,1260 -20_10037292_10066351 14458 . A . . END=14470 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 14471 . C . . END=14471 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,957 -20_10037292_10066351 14472 . T . . END=14473 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1032 -20_10037292_10066351 14474 . A . . END=14492 GT:DP:GQ:MIN_DP:PL 0/0:38:99:33:0,99,1015 -20_10037292_10066351 14493 . A . . END=14493 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1013 -20_10037292_10066351 14494 . A . . END=14495 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 14496 . T . . END=14496 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1103 -20_10037292_10066351 14497 . A . . END=14500 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 14501 . G . . END=14502 GT:DP:GQ:MIN_DP:PL 0/0:39:83:38:0,83,1070 -20_10037292_10066351 14503 . C . . END=14513 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,99,1485 -20_10037292_10066351 14514 . A . . END=14517 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 14518 . A . . END=14519 GT:DP:GQ:MIN_DP:PL 0/0:36:87:36:0,87,1305 -20_10037292_10066351 14520 . A . . END=14523 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 14524 . T . . END=14524 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1001 -20_10037292_10066351 14525 . T . . END=14527 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 14528 . T . . END=14528 GT:DP:GQ:MIN_DP:PL 0/0:32:67:32:0,67,931 -20_10037292_10066351 14529 . T . . END=14529 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,950 -20_10037292_10066351 14530 . T . . END=14530 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 14531 . A . . END=14548 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,99,1108 -20_10037292_10066351 14549 . C . . END=14549 GT:DP:GQ:MIN_DP:PL 0/0:40:83:40:0,83,1170 -20_10037292_10066351 14550 . A . . END=14557 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1665 -20_10037292_10066351 14558 . C . . END=14558 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1130 -20_10037292_10066351 14559 . C . . END=14609 GT:DP:GQ:MIN_DP:PL 0/0:45:99:40:0,101,1298 -20_10037292_10066351 14610 . A . . END=14610 GT:DP:GQ:MIN_DP:PL 0/0:44:92:44:0,92,1272 -20_10037292_10066351 14611 . C . . END=14683 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,99,1157 -20_10037292_10066351 14684 . T . . END=14684 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14685 . T . . END=14685 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 14686 . A . . END=14692 GT:DP:GQ:MIN_DP:PL 0/0:37:92:35:0,92,1073 -20_10037292_10066351 14693 . T . . END=14693 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 14694 . G . . END=14699 GT:DP:GQ:MIN_DP:PL 0/0:36:93:34:0,93,1109 -20_10037292_10066351 14700 . A . . END=14700 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1091 -20_10037292_10066351 14701 . T . . END=14701 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 14702 . T . . END=14702 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1053 -20_10037292_10066351 14703 . A . . END=14703 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 14704 . A . . END=14708 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 14709 . G . . END=14714 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14715 . A . . END=14715 GT:DP:GQ:MIN_DP:PL 0/0:36:86:36:0,86,1081 -20_10037292_10066351 14716 . C . . END=14717 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14718 . T . . END=14721 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 14722 . A . . END=14722 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1110 -20_10037292_10066351 14723 . T . . END=14725 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 14726 . A . . END=14726 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1117 -20_10037292_10066351 14727 . T . . END=14737 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1099 diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf.idx b/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf.idx deleted file mode 100644 index a641f33b6..000000000 Binary files a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf.idx and /dev/null differ diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf b/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf deleted file mode 100644 index 710aba049..000000000 --- a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf +++ /dev/null @@ -1,1676 +0,0 @@ -##fileformat=VCFv4.2 -##ALT= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) -##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) -##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) -##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) -##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) -##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) -##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) -##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) -##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) -##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) -##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) -##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) -##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) -##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) -##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) -##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) -##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) -##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) -##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) -##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) -##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) -##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) -##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) -##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) -##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) -##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) -##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) -##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) -##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) -##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) -##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) -##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) -##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) -##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) -##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) -##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) -##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) -##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) -##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) -##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) -##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) -##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) -##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) -##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) -##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) -##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) -##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) -##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) -##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) -##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) -##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) -##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) -##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) -##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) -##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) -##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) -##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) -##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) -##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) -##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) -##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) -##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) -##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) -##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) -##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive) -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_mother -20_10037292_10066351 3277 . G . . END=3278 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 3279 . A . . END=3279 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1084 -20_10037292_10066351 3280 . A . . END=3281 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 3282 . T . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 3283 . T . . END=3283 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 3284 . T . . END=3284 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 3285 . T . . END=3293 GT:DP:GQ:MIN_DP:PL 0/0:35:81:31:0,81,1215 -20_10037292_10066351 3294 . A . . END=3302 GT:DP:GQ:MIN_DP:PL 0/0:33:90:30:0,90,970 -20_10037292_10066351 3303 . G . . END=3304 GT:DP:GQ:MIN_DP:PL 0/0:33:72:32:0,72,963 -20_10037292_10066351 3305 . C . . END=3309 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1053 -20_10037292_10066351 3310 . A . . END=3319 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1086 -20_10037292_10066351 3320 . A . . END=3320 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,959 -20_10037292_10066351 3321 . A . . END=3322 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 3323 . G . . END=3323 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,953 -20_10037292_10066351 3324 . T . . END=3325 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 3326 . G . . END=3326 GT:DP:GQ:MIN_DP:PL 0/0:31:60:31:0,60,873 -20_10037292_10066351 3327 . C . . END=3328 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 3329 . T . . END=3329 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 3330 . G . . END=3330 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,949 -20_10037292_10066351 3331 . T . . END=3332 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 3333 . A . . END=3335 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,892 -20_10037292_10066351 3336 . T . . END=3337 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 3338 . C . . END=3338 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,851 -20_10037292_10066351 3339 . C . . END=3339 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 3340 . T . . END=3340 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,888 -20_10037292_10066351 3341 . A . . END=3343 GT:DP:GQ:MIN_DP:PL 0/0:30:84:28:0,84,910 -20_10037292_10066351 3344 . T . . END=3344 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,832 -20_10037292_10066351 3345 . T . . END=3348 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,891 -20_10037292_10066351 3349 . A . . END=3349 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,904 -20_10037292_10066351 3350 . G . . END=3350 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,910 -20_10037292_10066351 3351 . T . . END=3352 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,975 -20_10037292_10066351 3353 . G . . END=3354 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,846 -20_10037292_10066351 3355 . A . . END=3355 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,978 -20_10037292_10066351 3356 . T . . END=3357 GT:DP:GQ:MIN_DP:PL 0/0:31:67:31:0,67,916 -20_10037292_10066351 3358 . A . . END=3363 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1017 -20_10037292_10066351 3364 . G . . END=3364 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,947 -20_10037292_10066351 3365 . A . . END=3365 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3366 . C . . END=3366 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,963 -20_10037292_10066351 3367 . T . . END=3369 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 3370 . C . . END=3370 GT:DP:GQ:MIN_DP:PL 0/0:32:46:32:0,46,903 -20_10037292_10066351 3371 . A . . END=3371 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3372 . A . . END=3372 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,905 -20_10037292_10066351 3373 . A . . END=3374 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3375 . G . . END=3375 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,922 -20_10037292_10066351 3376 . C . . END=3376 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 3377 . A . . END=3381 GT:DP:GQ:MIN_DP:PL 0/0:32:84:31:0,84,1260 -20_10037292_10066351 3382 . A . . END=3385 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3386 . A . . END=3387 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,964 -20_10037292_10066351 3388 . A . . END=3397 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 3398 . A . . END=3398 GT:DP:GQ:MIN_DP:PL 0/0:31:75:31:0,75,920 -20_10037292_10066351 3399 . T . . END=3399 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3400 . T . . END=3400 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3401 . T . . END=3402 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 3403 . T . . END=3403 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3404 . C . . END=3405 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,944 -20_10037292_10066351 3406 . G . . END=3407 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,859 -20_10037292_10066351 3408 . G . . END=3408 GT:DP:GQ:MIN_DP:PL 0/0:32:62:32:0,62,890 -20_10037292_10066351 3409 . T . . END=3418 GT:DP:GQ:MIN_DP:PL 0/0:33:81:30:0,81,1215 -20_10037292_10066351 3419 . T . . END=3419 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,827 -20_10037292_10066351 3420 . T . . END=3421 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 3422 . T . . END=3430 GT:DP:GQ:MIN_DP:PL 0/0:29:75:28:0,75,1125 -20_10037292_10066351 3431 . T . . END=3439 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 3440 . A . . END=3440 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,782 -20_10037292_10066351 3441 . T . . END=3442 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 3443 . T . . END=3443 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3444 . T . . END=3445 GT:DP:GQ:MIN_DP:PL 0/0:28:64:28:0,64,722 -20_10037292_10066351 3446 . G . . END=3446 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3447 . C . . END=3447 GT:DP:GQ:MIN_DP:PL 0/0:29:53:29:0,53,694 -20_10037292_10066351 3448 . T . . END=3449 GT:DP:GQ:MIN_DP:PL 0/0:31:76:30:0,76,827 -20_10037292_10066351 3450 . A . . END=3450 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3451 . C . . END=3452 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,715 -20_10037292_10066351 3453 . T . . END=3455 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 3456 . A . . END=3456 GT:DP:GQ:MIN_DP:PL 0/0:31:23:31:0,23,766 -20_10037292_10066351 3457 . T . . END=3460 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3461 . C . . END=3461 GT:DP:GQ:MIN_DP:PL 0/0:30:89:30:0,89,873 -20_10037292_10066351 3462 . T . . END=3462 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3463 . G . . END=3463 GT:DP:GQ:MIN_DP:PL 0/0:31:44:31:0,44,739 -20_10037292_10066351 3464 . T . . END=3468 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3469 . C . . END=3469 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,816 -20_10037292_10066351 3470 . T . . END=3470 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 3471 . T . . END=3478 GT:DP:GQ:MIN_DP:PL 0/0:32:75:32:0,75,1125 -20_10037292_10066351 3479 . T . . END=3479 GT:DP:GQ:MIN_DP:PL 0/0:34:36:34:0,36,906 -20_10037292_10066351 3480 . C CT, 503.03 . DP=23;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=82800,23 GT:AD:DP:GQ:PL:SB 1/1:0,18,0:18:54:517,54,0,517,54,517:0,0,7,11 -20_10037292_10066351 3481 . T . . END=3481 GT:DP:GQ:MIN_DP:PL 0/0:21:51:21:0,51,765 -20_10037292_10066351 3482 . T . . END=3482 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 -20_10037292_10066351 3483 . T . . END=3487 GT:DP:GQ:MIN_DP:PL 0/0:20:51:19:0,51,765 -20_10037292_10066351 3488 . T . . END=3488 GT:DP:GQ:MIN_DP:PL 0/0:19:42:19:0,42,571 -20_10037292_10066351 3489 . A . . END=3489 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,521 -20_10037292_10066351 3490 . C . . END=3490 GT:DP:GQ:MIN_DP:PL 0/0:17:35:17:0,35,431 -20_10037292_10066351 3491 . A . . END=3495 GT:DP:GQ:MIN_DP:PL 0/0:17:48:17:0,48,720 -20_10037292_10066351 3496 . A . . END=3498 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,473 -20_10037292_10066351 3499 . C . . END=3499 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,428 -20_10037292_10066351 3500 . G . . END=3500 GT:DP:GQ:MIN_DP:PL 0/0:16:31:16:0,31,379 -20_10037292_10066351 3501 . T . . END=3501 GT:DP:GQ:MIN_DP:PL 0/0:17:48:17:0,48,720 -20_10037292_10066351 3502 . A . . END=3503 GT:DP:GQ:MIN_DP:PL 0/0:19:54:18:0,54,550 -20_10037292_10066351 3504 . T . . END=3504 GT:DP:GQ:MIN_DP:PL 0/0:19:48:19:0,48,720 -20_10037292_10066351 3505 . A . . END=3506 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 -20_10037292_10066351 3507 . T . . END=3519 GT:DP:GQ:MIN_DP:PL 0/0:19:54:18:0,54,501 -20_10037292_10066351 3520 . AT A, 609.03 . DP=18;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=64800,18 GT:AD:DP:GQ:PL:SB 1/1:0,18,0:18:54:623,54,0,623,54,623:0,0,9,9 -20_10037292_10066351 3522 . T . . END=3525 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,550 -20_10037292_10066351 3526 . T . . END=3527 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,607 -20_10037292_10066351 3528 . T . . END=3528 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20_10037292_10066351 3529 . T A, 155.64 . BaseQRankSum=-0.544;DP=21;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=75600,21;ReadPosRankSum=-1.158 GT:AD:DP:GQ:PL:SB 0/1:12,8,0:20:99:163,0,328,199,352,551:5,7,5,3 -20_10037292_10066351 3530 . A . . END=3530 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,941 -20_10037292_10066351 3531 . A . . END=3533 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 3534 . A . . END=3534 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1170 -20_10037292_10066351 3535 . A . . END=3536 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,891 -20_10037292_10066351 3537 . A . . END=3546 GT:DP:GQ:MIN_DP:PL 0/0:29:72:26:0,72,1080 -20_10037292_10066351 3547 . A . . END=3547 GT:DP:GQ:MIN_DP:PL 0/0:26:56:26:0,56,731 -20_10037292_10066351 3548 . G . . END=3549 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 3550 . T . . END=3553 GT:DP:GQ:MIN_DP:PL 0/0:26:60:25:0,60,707 -20_10037292_10066351 3554 . A . . END=3556 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 3557 . A . . END=3557 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 3558 . A . . END=3559 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,819 -20_10037292_10066351 3560 . G . . END=3560 GT:DP:GQ:MIN_DP:PL 0/0:27:54:27:0,54,721 -20_10037292_10066351 3561 . T . . END=3562 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 3563 . C . . END=3569 GT:DP:GQ:MIN_DP:PL 0/0:29:81:27:0,81,833 -20_10037292_10066351 3570 . C . . END=3570 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 3571 . C . . END=3571 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,788 -20_10037292_10066351 3572 . A . . END=3583 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 3584 . T . . END=3594 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,1125 -20_10037292_10066351 3595 . C . . END=3595 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 3596 . T . . END=3602 GT:DP:GQ:MIN_DP:PL 0/0:27:75:25:0,75,800 -20_10037292_10066351 3603 . T . . END=3603 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,824 -20_10037292_10066351 3604 . G . . END=3611 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 3612 . G . . END=3612 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,786 -20_10037292_10066351 3613 . T . . END=3613 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 3614 . G . . END=3614 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,825 -20_10037292_10066351 3615 . C . . END=3615 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 3616 . A . . END=3616 GT:DP:GQ:MIN_DP:PL 0/0:27:61:27:0,61,752 -20_10037292_10066351 3617 . T . . END=3617 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,774 -20_10037292_10066351 3618 . T . . END=3619 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 3620 . C . . END=3620 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,813 -20_10037292_10066351 3621 . A . . END=3638 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 -20_10037292_10066351 3639 . G . . END=3639 GT:DP:GQ:MIN_DP:PL 0/0:28:67:28:0,67,821 -20_10037292_10066351 3640 . A . . END=3640 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3641 . A . . END=3645 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 3646 . G . . END=3646 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,894 -20_10037292_10066351 3647 . C . . END=3649 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 3650 . A . . END=3650 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,922 -20_10037292_10066351 3651 . G . . END=3653 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3654 . T . . END=3654 GT:DP:GQ:MIN_DP:PL 0/0:29:60:29:0,60,844 -20_10037292_10066351 3655 . T . . END=3655 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 3656 . C . . END=3658 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 3659 . G . . END=3661 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3662 . C . . END=3662 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,961 -20_10037292_10066351 3663 . A . . END=3666 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,911 -20_10037292_10066351 3667 . G . . END=3667 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,943 -20_10037292_10066351 3668 . A . . END=3668 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3669 . T . . END=3669 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,897 -20_10037292_10066351 3670 . G . . END=3670 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,889 -20_10037292_10066351 3671 . T . . END=3671 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,947 -20_10037292_10066351 3672 . G . . END=3672 GT:DP:GQ:MIN_DP:PL 0/0:32:77:32:0,77,907 -20_10037292_10066351 3673 . T . . END=3676 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,869 -20_10037292_10066351 3677 . G . . END=3677 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,927 -20_10037292_10066351 3678 . G . . END=3679 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3680 . A . . END=3680 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,912 -20_10037292_10066351 3681 . G . . END=3684 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,977 -20_10037292_10066351 3685 . T . . END=3687 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3688 . C . . END=3688 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,891 -20_10037292_10066351 3689 . A . . END=3689 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,983 -20_10037292_10066351 3690 . G . . END=3691 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1003 -20_10037292_10066351 3692 . G . . END=3693 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1001 -20_10037292_10066351 3694 . A . . END=3694 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 3695 . G . . END=3695 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1051 -20_10037292_10066351 3696 . A . . END=3700 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 3701 . T . . END=3701 GT:DP:GQ:MIN_DP:PL 0/0:36:79:36:0,79,985 -20_10037292_10066351 3702 . A . . END=3702 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 3703 . T . . END=3703 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1054 -20_10037292_10066351 3704 . G . . END=3704 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 3705 . G . . END=3706 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1107 -20_10037292_10066351 3707 . G . . END=3707 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 3708 . T . . END=3708 GT:DP:GQ:MIN_DP:PL 0/0:37:57:37:0,57,902 -20_10037292_10066351 3709 . G . . END=3715 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 3716 . A . . END=3724 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,1056 -20_10037292_10066351 3725 . G . . END=3725 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1033 -20_10037292_10066351 3726 . A . . END=3726 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 3727 . C . . END=3727 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,925 -20_10037292_10066351 3728 . A . . END=3728 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3729 . C . . END=3729 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,930 -20_10037292_10066351 3730 . G . . END=3732 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,947 -20_10037292_10066351 3733 . A . . END=3733 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1034 -20_10037292_10066351 3734 . A . . END=3736 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1074 -20_10037292_10066351 3737 . A . . END=3742 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 3743 . G . . END=3743 GT:DP:GQ:MIN_DP:PL 0/0:35:83:35:0,83,1077 -20_10037292_10066351 3744 . C . . END=3744 GT:DP:GQ:MIN_DP:PL 0/0:36:59:36:0,59,1005 -20_10037292_10066351 3745 . C . . END=3750 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1058 -20_10037292_10066351 3751 . A . . END=3751 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 3752 . G . . END=3754 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 3755 . T . . END=3755 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1030 -20_10037292_10066351 3756 . G . . END=3758 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 3759 . C . . END=3761 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 3762 . T . . END=3762 GT:DP:GQ:MIN_DP:PL 0/0:37:70:37:0,70,1061 -20_10037292_10066351 3763 . C . . END=3763 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1147 -20_10037292_10066351 3764 . A . . END=3767 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 3768 . G . . END=3768 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1166 -20_10037292_10066351 3769 . A . . END=3770 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 3771 . A . . END=3771 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1049 -20_10037292_10066351 3772 . C . . END=3772 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 3773 . C . . END=3773 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1116 -20_10037292_10066351 3774 . A . . END=3780 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1199 -20_10037292_10066351 3781 . C . . END=3781 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1169 -20_10037292_10066351 3782 . T . . END=3792 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 3793 . T . . END=3795 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3796 . G . . END=3796 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1000 -20_10037292_10066351 3797 . G . . END=3814 GT:DP:GQ:MIN_DP:PL 0/0:35:93:32:0,93,1021 -20_10037292_10066351 3815 . A . . END=3825 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1007 -20_10037292_10066351 3826 . C . . END=3827 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 3828 . T . . END=3848 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 3849 . G . . END=3856 GT:DP:GQ:MIN_DP:PL 0/0:29:78:27:0,78,1170 -20_10037292_10066351 3857 . A . . END=3867 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,816 -20_10037292_10066351 3868 . T . . END=3868 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,891 -20_10037292_10066351 3869 . G . . END=3880 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3881 . C . . END=3882 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,978 -20_10037292_10066351 3883 . G . . END=3883 GT:DP:GQ:MIN_DP:PL 0/0:30:89:30:0,89,918 -20_10037292_10066351 3884 . T . . END=3892 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,994 -20_10037292_10066351 3893 . T . . END=3893 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1072 -20_10037292_10066351 3894 . C . . END=3898 GT:DP:GQ:MIN_DP:PL 0/0:33:93:31:0,93,882 -20_10037292_10066351 3899 . G . . END=3899 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 3900 . C . . END=3903 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 -20_10037292_10066351 3904 . T . . END=3904 GT:DP:GQ:MIN_DP:PL 0/0:36:77:36:0,77,1073 -20_10037292_10066351 3905 . C . . END=3910 GT:DP:GQ:MIN_DP:PL 0/0:37:93:36:0,93,1395 -20_10037292_10066351 3911 . A . . END=3911 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3912 . G . . END=3912 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 3913 . G . . END=3914 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3915 . C . . END=3920 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 3921 . G . . END=3937 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1052 -20_10037292_10066351 3938 . A . . END=3938 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1028 -20_10037292_10066351 3939 . A . . END=3942 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 3943 . T . . END=3949 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 3950 . G . . END=3954 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1050 -20_10037292_10066351 3955 . A . . END=3955 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 3956 . A . . END=3958 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3959 . G . . END=3959 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1117 -20_10037292_10066351 3960 . C . . END=3960 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,902 -20_10037292_10066351 3961 . G . . END=4011 GT:DP:GQ:MIN_DP:PL 0/0:40:99:34:0,102,1024 -20_10037292_10066351 4012 . C T, 1398.06 . DP=44;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=158400,44 GT:AD:DP:GQ:PL:SB 1/1:0,43,0:43:99:1412,129,0,1412,129,1412:0,0,21,22 -20_10037292_10066351 4013 . G . . END=4023 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,106,1268 -20_10037292_10066351 4024 . T . . END=4024 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1212 -20_10037292_10066351 4025 . A . . END=4057 GT:DP:GQ:MIN_DP:PL 0/0:41:99:35:0,102,1223 -20_10037292_10066351 4058 . T . . END=4058 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1090 -20_10037292_10066351 4059 . T . . END=4081 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1106 -20_10037292_10066351 4082 . C . . END=4085 GT:DP:GQ:MIN_DP:PL 0/0:36:96:35:0,96,1440 -20_10037292_10066351 4086 . A . . END=4086 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4087 . T . . END=4089 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 4090 . A . . END=4095 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4096 . T . . END=4114 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 4115 . T . . END=4115 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1024 -20_10037292_10066351 4116 . T . . END=4116 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4117 . A . . END=4119 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 4120 . A . . END=4121 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 4122 . G . . END=4123 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 4124 . G . . END=4131 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,986 -20_10037292_10066351 4132 . T . . END=4133 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,1060 -20_10037292_10066351 4134 . C . . END=4134 GT:DP:GQ:MIN_DP:PL 0/0:32:47:32:0,47,810 -20_10037292_10066351 4135 . G . . END=4136 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 4137 . A . . END=4137 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,899 -20_10037292_10066351 4138 . T . . END=4141 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4142 . A . . END=4142 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1001 -20_10037292_10066351 4143 . T . . END=4149 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 4150 . T . . END=4150 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,947 -20_10037292_10066351 4151 . A . . END=4157 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 4158 . G . . END=4158 GT:DP:GQ:MIN_DP:PL 0/0:32:24:32:0,24,861 -20_10037292_10066351 4159 . G . . END=4159 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,982 -20_10037292_10066351 4160 . A . . END=4164 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1052 -20_10037292_10066351 4165 . A . . END=4167 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 4168 . A . . END=4168 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,1046 -20_10037292_10066351 4169 . C . . END=4169 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 4170 . G . . END=4172 GT:DP:GQ:MIN_DP:PL 0/0:38:96:37:0,96,1440 -20_10037292_10066351 4173 . C . . END=4174 GT:DP:GQ:MIN_DP:PL 0/0:37:75:37:0,75,1090 -20_10037292_10066351 4175 . T . . END=4175 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1052 -20_10037292_10066351 4176 . C . . END=4182 GT:DP:GQ:MIN_DP:PL 0/0:33:91:32:0,91,1105 -20_10037292_10066351 4183 . C . . END=4184 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1094 -20_10037292_10066351 4185 . C . . END=4185 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 4186 . T . . END=4186 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1062 -20_10037292_10066351 4187 . T . . END=4188 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 4189 . T . . END=4189 GT:DP:GQ:MIN_DP:PL 0/0:33:88:33:0,88,1038 -20_10037292_10066351 4190 . G . . END=4202 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 4203 . A . . END=4224 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 4225 . A . . END=4226 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 4227 . T . . END=4234 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4235 . C . . END=4235 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,980 -20_10037292_10066351 4236 . A . . END=4236 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4237 . T . . END=4241 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4242 . G . . END=4242 GT:DP:GQ:MIN_DP:PL 0/0:30:61:30:0,61,914 -20_10037292_10066351 4243 . G . . END=4243 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4244 . T . . END=4244 GT:DP:GQ:MIN_DP:PL 0/0:30:71:30:0,71,911 -20_10037292_10066351 4245 . T . . END=4245 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4246 . G . . END=4249 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,979 -20_10037292_10066351 4250 . G . . END=4255 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 4256 . A . . END=4260 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4261 . G . . END=4263 GT:DP:GQ:MIN_DP:PL 0/0:32:83:31:0,83,1010 -20_10037292_10066351 4264 . T . . END=4264 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4265 . G . . END=4265 GT:DP:GQ:MIN_DP:PL 0/0:33:79:33:0,79,998 -20_10037292_10066351 4266 . T . . END=4269 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 4270 . T . . END=4271 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 4272 . A . . END=4275 GT:DP:GQ:MIN_DP:PL 0/0:34:87:31:0,87,1305 -20_10037292_10066351 4276 . T . . END=4276 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,961 -20_10037292_10066351 4277 . C . . END=4280 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4281 . T . . END=4281 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,942 -20_10037292_10066351 4282 . A . . END=4283 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 4284 . T . . END=4285 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4286 . T . . END=4286 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 4287 . C . . END=4287 GT:DP:GQ:MIN_DP:PL 0/0:33:59:33:0,59,989 -20_10037292_10066351 4288 . T . . END=4288 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 4289 . A . . END=4293 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 4294 . A . . END=4296 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 4297 . A . . END=4302 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1005 -20_10037292_10066351 4303 . C . . END=4303 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4304 . C . . END=4321 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 4322 . G . . END=4323 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 4324 . A . . END=4329 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 4330 . G . . END=4330 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4331 . A . . END=4331 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,963 -20_10037292_10066351 4332 . C . . END=4332 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1015 -20_10037292_10066351 4333 . C . . END=4333 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4334 . C . . END=4334 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1006 -20_10037292_10066351 4335 . A . . END=4337 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1133 -20_10037292_10066351 4338 . C . . END=4338 GT:DP:GQ:MIN_DP:PL 0/0:36:56:36:0,56,988 -20_10037292_10066351 4339 . C . . END=4339 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1032 -20_10037292_10066351 4340 . T . . END=4340 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4341 . G . . END=4341 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1141 -20_10037292_10066351 4342 . A . . END=4343 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,105,1076 -20_10037292_10066351 4344 . C . . END=4345 GT:DP:GQ:MIN_DP:PL 0/0:37:73:36:0,73,1097 -20_10037292_10066351 4346 . G . . END=4346 GT:DP:GQ:MIN_DP:PL 0/0:36:59:36:0,59,1017 -20_10037292_10066351 4347 . T . . END=4349 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1083 -20_10037292_10066351 4350 . G . . END=4350 GT:DP:GQ:MIN_DP:PL 0/0:37:83:37:0,83,1083 -20_10037292_10066351 4351 . A . . END=4354 GT:DP:GQ:MIN_DP:PL 0/0:37:76:37:0,76,1062 -20_10037292_10066351 4355 . G . . END=4355 GT:DP:GQ:MIN_DP:PL 0/0:37:62:37:0,62,1004 -20_10037292_10066351 4356 . A . . END=4356 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1081 -20_10037292_10066351 4357 . A . . END=4357 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1116 -20_10037292_10066351 4358 . A . . END=4358 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1094 -20_10037292_10066351 4359 . A . . END=4359 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4360 . G . . END=4363 GT:DP:GQ:MIN_DP:PL 0/0:37:73:36:0,73,1042 -20_10037292_10066351 4364 . T . . END=4364 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1082 -20_10037292_10066351 4365 . C . . END=4366 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1056 -20_10037292_10066351 4367 . T . . END=4367 GT:DP:GQ:MIN_DP:PL 0/0:37:63:37:0,63,1057 -20_10037292_10066351 4368 . G . . END=4368 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1014 -20_10037292_10066351 4369 . G . . END=4369 GT:DP:GQ:MIN_DP:PL 0/0:37:65:37:0,65,1058 -20_10037292_10066351 4370 . A . . END=4370 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,1028 -20_10037292_10066351 4371 . G . . END=4375 GT:DP:GQ:MIN_DP:PL 0/0:37:74:36:0,74,1002 -20_10037292_10066351 4376 . T . . END=4376 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,933 -20_10037292_10066351 4377 . T . . END=4377 GT:DP:GQ:MIN_DP:PL 0/0:33:52:33:0,52,895 -20_10037292_10066351 4378 . C . . END=4378 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1050 -20_10037292_10066351 4379 . A . . END=4379 GT:DP:GQ:MIN_DP:PL 0/0:34:53:34:0,53,926 -20_10037292_10066351 4380 . C . . END=4381 GT:DP:GQ:MIN_DP:PL 0/0:34:65:33:0,65,983 -20_10037292_10066351 4382 . T . . END=4382 GT:DP:GQ:MIN_DP:PL 0/0:34:54:34:0,54,901 -20_10037292_10066351 4383 . T . . END=4386 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,976 -20_10037292_10066351 4387 . A . . END=4387 GT:DP:GQ:MIN_DP:PL 0/0:33:40:33:0,40,800 -20_10037292_10066351 4388 . C . . END=4388 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,926 -20_10037292_10066351 4389 . C . . END=4389 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,980 -20_10037292_10066351 4390 . A . . END=4390 GT:DP:GQ:MIN_DP:PL 0/0:34:54:34:0,54,915 -20_10037292_10066351 4391 . T . . END=4391 GT:DP:GQ:MIN_DP:PL 0/0:34:52:34:0,52,819 -20_10037292_10066351 4392 . C . . END=4393 GT:DP:GQ:MIN_DP:PL 0/0:33:62:32:0,62,824 -20_10037292_10066351 4394 . A . . END=4396 GT:DP:GQ:MIN_DP:PL 0/0:36:71:35:0,71,987 -20_10037292_10066351 4397 . T . . END=4398 GT:DP:GQ:MIN_DP:PL 0/0:37:61:36:0,61,1000 -20_10037292_10066351 4399 . A . . END=4399 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 4400 . T . . END=4400 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1063 -20_10037292_10066351 4401 . T . . END=4402 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1098 -20_10037292_10066351 4403 . A . . END=4403 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 4404 . A . . END=4404 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 4405 . A . . END=4405 GT:DP:GQ:MIN_DP:PL 0/0:38:80:38:0,80,1107 -20_10037292_10066351 4406 . C . . END=4406 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,945 -20_10037292_10066351 4407 . A . . END=4407 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4408 . T . . END=4408 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 4409 . A ATG,ATATG, 710.03 . DP=31;ExcessHet=0.0000;MLEAC=0,2,0;MLEAF=0.00,1.00,0.00;RAW_MQandDP=111600,31 GT:AD:DP:GQ:PL:SB 2/2:0,0,21,0:21:69:724,765,1112,69,87,0,767,961,90,918:0,0,10,11 -20_10037292_10066351 4410 . T . . END=4410 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1170 -20_10037292_10066351 4411 . G . . END=4411 GT:DP:GQ:MIN_DP:PL 0/0:39:0:39:0,0,531 -20_10037292_10066351 4412 . T . . END=4419 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1260 -20_10037292_10066351 4420 . T . . END=4426 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 4427 . G . . END=4427 GT:DP:GQ:MIN_DP:PL 0/0:36:74:36:0,74,1020 -20_10037292_10066351 4428 . T . . END=4431 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1260 -20_10037292_10066351 4432 . T . . END=4435 GT:DP:GQ:MIN_DP:PL 0/0:37:90:35:0,90,1350 -20_10037292_10066351 4436 . C . . END=4436 GT:DP:GQ:MIN_DP:PL 0/0:35:0:35:0,0,717 -20_10037292_10066351 4437 . A . . END=4437 GT:DP:GQ:MIN_DP:PL 0/0:35:34:35:0,34,781 -20_10037292_10066351 4438 . T . . END=4438 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 4439 . G . . END=4454 GT:DP:GQ:MIN_DP:PL 0/0:33:81:31:0,81,971 -20_10037292_10066351 4455 . A . . END=4455 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4456 . T . . END=4462 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,927 -20_10037292_10066351 4463 . A . . END=4463 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,936 -20_10037292_10066351 4464 . T . . END=4465 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 4466 . T . . END=4473 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 4474 . A . . END=4474 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,890 -20_10037292_10066351 4475 . G . . END=4475 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,869 -20_10037292_10066351 4476 . A . . END=4476 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,879 -20_10037292_10066351 4477 . C . . END=4484 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,860 -20_10037292_10066351 4485 . C . . END=4485 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,887 -20_10037292_10066351 4486 . A . . END=4487 GT:DP:GQ:MIN_DP:PL 0/0:32:84:31:0,84,1260 -20_10037292_10066351 4488 . G . . END=4488 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,942 -20_10037292_10066351 4489 . G . . END=4491 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 4492 . C . . END=4492 GT:DP:GQ:MIN_DP:PL 0/0:29:56:29:0,56,779 -20_10037292_10066351 4493 . G . . END=4493 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,804 -20_10037292_10066351 4494 . C . . END=4495 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,950 -20_10037292_10066351 4496 . G . . END=4496 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,925 -20_10037292_10066351 4497 . T . . END=4499 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,963 -20_10037292_10066351 4500 . C . . END=4500 GT:DP:GQ:MIN_DP:PL 0/0:29:67:29:0,67,843 -20_10037292_10066351 4501 . A . . END=4504 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4505 . T . . END=4507 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,952 -20_10037292_10066351 4508 . C . . END=4508 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,892 -20_10037292_10066351 4509 . A . . END=4509 GT:DP:GQ:MIN_DP:PL 0/0:31:73:31:0,73,943 -20_10037292_10066351 4510 . G . . END=4510 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,954 -20_10037292_10066351 4511 . T . . END=4511 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,878 -20_10037292_10066351 4512 . T . . END=4512 GT:DP:GQ:MIN_DP:PL 0/0:31:60:31:0,60,895 -20_10037292_10066351 4513 . C . . END=4513 GT:DP:GQ:MIN_DP:PL 0/0:32:47:32:0,47,858 -20_10037292_10066351 4514 . A . . END=4516 GT:DP:GQ:MIN_DP:PL 0/0:32:62:32:0,62,916 -20_10037292_10066351 4517 . G . . END=4517 GT:DP:GQ:MIN_DP:PL 0/0:32:34:32:0,34,834 -20_10037292_10066351 4518 . C . . END=4518 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,949 -20_10037292_10066351 4519 . A . . END=4519 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,970 -20_10037292_10066351 4520 . A . . END=4520 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,932 -20_10037292_10066351 4521 . C . . END=4521 GT:DP:GQ:MIN_DP:PL 0/0:32:50:32:0,50,885 -20_10037292_10066351 4522 . C . . END=4522 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1000 -20_10037292_10066351 4523 . T . . END=4524 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1056 -20_10037292_10066351 4525 . C . . END=4525 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,931 -20_10037292_10066351 4526 . A . . END=4526 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,862 -20_10037292_10066351 4527 . C . . END=4527 GT:DP:GQ:MIN_DP:PL 0/0:32:49:32:0,49,875 -20_10037292_10066351 4528 . C . . END=4530 GT:DP:GQ:MIN_DP:PL 0/0:33:65:33:0,65,945 -20_10037292_10066351 4531 . C . . END=4533 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 -20_10037292_10066351 4534 . G . . END=4534 GT:DP:GQ:MIN_DP:PL 0/0:33:71:33:0,71,931 -20_10037292_10066351 4535 . G . . END=4548 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,924 -20_10037292_10066351 4549 . C . . END=4555 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,875 -20_10037292_10066351 4556 . C . . END=4564 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 4565 . G . . END=4565 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,769 -20_10037292_10066351 4566 . A . . END=4566 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,945 -20_10037292_10066351 4567 . T . . END=4568 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 4569 . T . . END=4574 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4575 . A . . END=4575 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1044 -20_10037292_10066351 4576 . T . . END=4582 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1077 -20_10037292_10066351 4583 . T . . END=4583 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,949 -20_10037292_10066351 4584 . A . . END=4584 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1036 -20_10037292_10066351 4585 . G . . END=4585 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,992 -20_10037292_10066351 4586 . A . . END=4586 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 4587 . G . . END=4587 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1042 -20_10037292_10066351 4588 . A . . END=4588 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,987 -20_10037292_10066351 4589 . T . . END=4589 GT:DP:GQ:MIN_DP:PL 0/0:35:60:35:0,60,992 -20_10037292_10066351 4590 . G . . END=4590 GT:DP:GQ:MIN_DP:PL 0/0:35:79:35:0,79,1008 -20_10037292_10066351 4591 . G . . END=4591 GT:DP:GQ:MIN_DP:PL 0/0:35:56:35:0,56,909 -20_10037292_10066351 4592 . G . . END=4593 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4594 . T . . END=4594 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,979 -20_10037292_10066351 4595 . T . . END=4596 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4597 . C . . END=4597 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,951 -20_10037292_10066351 4598 . A . . END=4599 GT:DP:GQ:MIN_DP:PL 0/0:35:66:34:0,66,937 -20_10037292_10066351 4600 . C . . END=4600 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,937 -20_10037292_10066351 4601 . A . . END=4603 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1025 -20_10037292_10066351 4604 . T . . END=4604 GT:DP:GQ:MIN_DP:PL 0/0:34:80:34:0,80,1029 -20_10037292_10066351 4605 . T . . END=4605 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 4606 . G . . END=4606 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,938 -20_10037292_10066351 4607 . G . . END=4607 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,966 -20_10037292_10066351 4608 . C . . END=4611 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 4612 . G . . END=4612 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,998 -20_10037292_10066351 4613 . C . . END=4616 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 4617 . T . . END=4620 GT:DP:GQ:MIN_DP:PL 0/0:33:81:28:0,81,853 -20_10037292_10066351 4621 . G . . END=4621 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4622 . A . . END=4626 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 4627 . C . . END=4627 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4628 . T . . END=4630 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 4631 . C . . END=4631 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4632 . C . . END=4632 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,940 -20_10037292_10066351 4633 . T . . END=4633 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4634 . C . . END=4634 GT:DP:GQ:MIN_DP:PL 0/0:31:60:31:0,60,922 -20_10037292_10066351 4635 . A . . END=4635 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,947 -20_10037292_10066351 4636 . A . . END=4636 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,1000 -20_10037292_10066351 4637 . G . . END=4637 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4638 . T . . END=4638 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,947 -20_10037292_10066351 4639 . G . . END=4639 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,968 -20_10037292_10066351 4640 . A . . END=4642 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4643 . C . . END=4644 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 4645 . C . . END=4649 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 4650 . T . . END=4650 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,874 -20_10037292_10066351 4651 . T . . END=4654 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,1080 -20_10037292_10066351 4655 . C . . END=4655 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,1035 -20_10037292_10066351 4656 . C . . END=4666 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,759 -20_10037292_10066351 4667 . C . . END=4668 GT:DP:GQ:MIN_DP:PL 0/0:27:61:26:0,61,735 -20_10037292_10066351 4669 . G . . END=4671 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,870 -20_10037292_10066351 4672 . A . . END=4672 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,840 -20_10037292_10066351 4673 . T . . END=4674 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,854 -20_10037292_10066351 4675 . A . . END=4675 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 4676 . C . . END=4677 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,802 -20_10037292_10066351 4678 . G . . END=4678 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,893 -20_10037292_10066351 4679 . G . . END=4686 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 4687 . C . . END=4687 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,884 -20_10037292_10066351 4688 . A . . END=4694 GT:DP:GQ:MIN_DP:PL 0/0:30:81:27:0,81,769 -20_10037292_10066351 4695 . C . . END=4695 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,879 -20_10037292_10066351 4696 . T . . END=4697 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 4698 . G . . END=4703 GT:DP:GQ:MIN_DP:PL 0/0:32:75:31:0,75,892 -20_10037292_10066351 4704 . A . . END=4709 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 4710 . T . . END=4711 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,855 -20_10037292_10066351 4712 . G . . END=4715 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 4716 . T . . END=4716 GT:DP:GQ:MIN_DP:PL 0/0:33:55:33:0,55,937 -20_10037292_10066351 4717 . T . . END=4724 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1084 -20_10037292_10066351 4725 . C . . END=4725 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1064 -20_10037292_10066351 4726 . A . . END=4735 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1264 -20_10037292_10066351 4736 . A . . END=4736 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1108 -20_10037292_10066351 4737 . C . . END=4749 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,111,1303 -20_10037292_10066351 4750 . C . . END=4750 GT:DP:GQ:MIN_DP:PL 0/0:42:96:42:0,96,1256 -20_10037292_10066351 4751 . T . . END=4790 GT:DP:GQ:MIN_DP:PL 0/0:44:99:41:0,104,1266 -20_10037292_10066351 4791 . G . . END=4791 GT:DP:GQ:MIN_DP:PL 0/0:45:78:45:0,78,1259 -20_10037292_10066351 4792 . A . . END=4802 GT:DP:GQ:MIN_DP:PL 0/0:45:99:44:0,107,1378 -20_10037292_10066351 4803 . A . . END=4803 GT:DP:GQ:MIN_DP:PL 0/0:44:83:44:0,83,1198 -20_10037292_10066351 4804 . A . . END=4810 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,114,1431 -20_10037292_10066351 4811 . T . . END=4811 GT:DP:GQ:MIN_DP:PL 0/0:45:79:45:0,79,1233 -20_10037292_10066351 4812 . A . . END=4831 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,101,1192 -20_10037292_10066351 4832 . C . . END=4833 GT:DP:GQ:MIN_DP:PL 0/0:43:95:43:0,95,1171 -20_10037292_10066351 4834 . C . . END=4849 GT:DP:GQ:MIN_DP:PL 0/0:43:99:39:0,99,1131 -20_10037292_10066351 4850 . A . . END=4851 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1137 -20_10037292_10066351 4852 . T . . END=4854 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 4855 . C . . END=4855 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1139 -20_10037292_10066351 4856 . T . . END=4859 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,1170 -20_10037292_10066351 4860 . T . . END=4866 GT:DP:GQ:MIN_DP:PL 0/0:36:81:34:0,81,1215 -20_10037292_10066351 4867 . T . . END=4876 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,1080 -20_10037292_10066351 4877 . G . . END=4887 GT:DP:GQ:MIN_DP:PL 0/0:26:63:25:0,63,766 -20_10037292_10066351 4888 . A . . END=4890 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 4891 . T . . END=4893 GT:DP:GQ:MIN_DP:PL 0/0:25:66:25:0,66,990 -20_10037292_10066351 4894 . C . . END=4894 GT:DP:GQ:MIN_DP:PL 0/0:25:59:25:0,59,757 -20_10037292_10066351 4895 . T . . END=4899 GT:DP:GQ:MIN_DP:PL 0/0:25:60:24:0,60,900 -20_10037292_10066351 4900 . A . . END=4913 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,813 -20_10037292_10066351 4914 . G . . END=4914 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 -20_10037292_10066351 4915 . G . . END=4915 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 4916 . G . . END=4919 GT:DP:GQ:MIN_DP:PL 0/0:27:65:26:0,65,769 -20_10037292_10066351 4920 . T . . END=4924 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 4925 . T . . END=4925 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 4926 . G . . END=4926 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 4927 . C . . END=4927 GT:DP:GQ:MIN_DP:PL 0/0:25:28:25:0,28,665 -20_10037292_10066351 4928 . A . . END=4928 GT:DP:GQ:MIN_DP:PL 0/0:25:47:25:0,47,725 -20_10037292_10066351 4929 . A . . END=4935 GT:DP:GQ:MIN_DP:PL 0/0:25:69:24:0,69,1035 -20_10037292_10066351 4936 . T . . END=4936 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,709 -20_10037292_10066351 4937 . A . . END=4939 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 4940 . A . . END=4940 GT:DP:GQ:MIN_DP:PL 0/0:24:56:24:0,56,727 -20_10037292_10066351 4941 . A . . END=4941 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4942 . G . . END=4942 GT:DP:GQ:MIN_DP:PL 0/0:24:40:24:0,40,714 -20_10037292_10066351 4943 . A . . END=4943 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4944 . A . . END=4949 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,737 -20_10037292_10066351 4950 . A . . END=4950 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4951 . T . . END=4951 GT:DP:GQ:MIN_DP:PL 0/0:24:56:24:0,56,685 -20_10037292_10066351 4952 . G . . END=4952 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 4953 . T . . END=4953 GT:DP:GQ:MIN_DP:PL 0/0:25:62:25:0,62,712 -20_10037292_10066351 4954 . C . . END=4959 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 4960 . A . . END=4962 GT:DP:GQ:MIN_DP:PL 0/0:29:84:28:0,84,876 -20_10037292_10066351 4963 . A . . END=4963 GT:DP:GQ:MIN_DP:PL 0/0:30:62:30:0,62,862 -20_10037292_10066351 4964 . G . . END=4966 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,955 -20_10037292_10066351 4967 . A . . END=4968 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 4969 . G . . END=4969 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,959 -20_10037292_10066351 4970 . C . . END=4970 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 4971 . A . . END=4971 GT:DP:GQ:MIN_DP:PL 0/0:30:44:30:0,44,863 -20_10037292_10066351 4972 . G . . END=4972 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,921 -20_10037292_10066351 4973 . A . . END=4976 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 4977 . A . . END=4977 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,903 -20_10037292_10066351 4978 . A . . END=4989 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,860 -20_10037292_10066351 4990 . T . . END=4990 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,837 -20_10037292_10066351 4991 . C . . END=5000 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 5001 . G . . END=5011 GT:DP:GQ:MIN_DP:PL 0/0:28:71:27:0,71,806 -20_10037292_10066351 5012 . A . . END=5012 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,831 -20_10037292_10066351 5013 . G . . END=5018 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 5019 . C . . END=5019 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,798 -20_10037292_10066351 5020 . A . . END=5026 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,793 -20_10037292_10066351 5027 . C T, 784.06 . DP=27;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=97200,27 GT:AD:DP:GQ:PL:SB 1/1:0,26,0:26:77:798,77,0,798,77,798:0,0,13,13 -20_10037292_10066351 5028 . C . . END=5037 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,905 -20_10037292_10066351 5038 . T . . END=5044 GT:DP:GQ:MIN_DP:PL 0/0:26:62:25:0,62,765 -20_10037292_10066351 5045 . G . . END=5045 GT:DP:GQ:MIN_DP:PL 0/0:27:58:27:0,58,808 -20_10037292_10066351 5046 . A . . END=5049 GT:DP:GQ:MIN_DP:PL 0/0:26:63:23:0,63,681 -20_10037292_10066351 5050 . T . . END=5050 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,633 -20_10037292_10066351 5051 . T . . END=5051 GT:DP:GQ:MIN_DP:PL 0/0:24:59:24:0,59,681 -20_10037292_10066351 5052 . G . . END=5055 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,722 -20_10037292_10066351 5056 . G . . END=5056 GT:DP:GQ:MIN_DP:PL 0/0:25:62:25:0,62,771 -20_10037292_10066351 5057 . A . . END=5057 GT:DP:GQ:MIN_DP:PL 0/0:25:75:25:0,75,713 -20_10037292_10066351 5058 . T . . END=5058 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,732 -20_10037292_10066351 5059 . G . . END=5059 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 5060 . A . . END=5060 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,709 -20_10037292_10066351 5061 . A . . END=5061 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,776 -20_10037292_10066351 5062 . T . . END=5063 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,874 -20_10037292_10066351 5064 . G . . END=5064 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,871 -20_10037292_10066351 5065 . A . . END=5069 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,838 -20_10037292_10066351 5070 . C . . END=5071 GT:DP:GQ:MIN_DP:PL 0/0:28:62:28:0,62,836 -20_10037292_10066351 5072 . G . . END=5072 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 5073 . A . . END=5074 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,851 -20_10037292_10066351 5075 . G . . END=5075 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,811 -20_10037292_10066351 5076 . T . . END=5078 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 5079 . G . . END=5079 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,837 -20_10037292_10066351 5080 . T . . END=5080 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 5081 . C . . END=5081 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,867 -20_10037292_10066351 5082 . C . . END=5087 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 5088 . A . . END=5088 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 5089 . G . . END=5095 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 5096 . G . . END=5097 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 5098 . A . . END=5103 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 5104 . C . . END=5106 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 5107 . G . . END=5108 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 5109 . T . . END=5109 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,899 -20_10037292_10066351 5110 . A . . END=5110 GT:DP:GQ:MIN_DP:PL 0/0:29:59:29:0,59,846 -20_10037292_10066351 5111 . C . . END=5129 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,876 -20_10037292_10066351 5130 . A . . END=5130 GT:DP:GQ:MIN_DP:PL 0/0:28:65:28:0,65,831 -20_10037292_10066351 5131 . T . . END=5134 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,843 -20_10037292_10066351 5135 . C . . END=5141 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,949 -20_10037292_10066351 5142 . C . . END=5142 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,965 -20_10037292_10066351 5143 . T . . END=5149 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 5150 . G . . END=5171 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,906 -20_10037292_10066351 5172 . C . . END=5172 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,921 -20_10037292_10066351 5173 . C . . END=5176 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 5177 . C . . END=5183 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 5184 . G . . END=5184 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,946 -20_10037292_10066351 5185 . C . . END=5189 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 5190 . T . . END=5190 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5191 . G . . END=5193 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5194 . T . . END=5196 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5197 . G . . END=5210 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 5211 . A . . END=5468 GT:DP:GQ:MIN_DP:PL 0/0:46:99:36:0,99,1192 -20_10037292_10066351 5469 . A G, 1297.06 . DP=42;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=151200,42 GT:AD:DP:GQ:PL:SB 1/1:0,42,0:42:99:1311,126,0,1311,126,1311:0,0,18,24 -20_10037292_10066351 5470 . G . . END=5495 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,111,1345 -20_10037292_10066351 7536 . C . . END=7552 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,107,1241 -20_10037292_10066351 7553 . A . . END=7553 GT:DP:GQ:MIN_DP:PL 0/0:41:78:41:0,78,1102 -20_10037292_10066351 7554 . A . . END=7555 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,102,1209 -20_10037292_10066351 7556 . C . . END=7556 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1063 -20_10037292_10066351 7557 . A G, 935.06 . DP=36;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=129600,36 GT:AD:DP:GQ:PL:SB 1/1:0,34,0:34:99:949,100,0,949,100,949:0,0,17,17 -20_10037292_10066351 7558 . C . . END=7558 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 7559 . T . . END=7559 GT:DP:GQ:MIN_DP:PL 0/0:38:94:38:0,94,1183 -20_10037292_10066351 7560 . C . . END=7569 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7570 . C . . END=7570 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1111 -20_10037292_10066351 7571 . A . . END=7573 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1138 -20_10037292_10066351 7574 . T . . END=7574 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1087 -20_10037292_10066351 7575 . T . . END=7579 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1069 -20_10037292_10066351 7580 . C . . END=7580 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1164 -20_10037292_10066351 7581 . T . . END=7581 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 7582 . T . . END=7582 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1088 -20_10037292_10066351 7583 . C . . END=7584 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 7585 . G . . END=7585 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 7586 . A . . END=7595 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,99,1485 -20_10037292_10066351 7596 . A . . END=7601 GT:DP:GQ:MIN_DP:PL 0/0:37:96:36:0,96,1440 -20_10037292_10066351 7602 . G . . END=7610 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7611 . A . . END=7611 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1069 -20_10037292_10066351 7612 . G . . END=7614 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1207 -20_10037292_10066351 7615 . C . . END=7615 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1080 -20_10037292_10066351 7616 . A . . END=7618 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7619 . T . . END=7630 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1395 -20_10037292_10066351 7631 . T . . END=7632 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 7633 . A . . END=7633 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1005 -20_10037292_10066351 7634 . G . . END=7649 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 7650 . A . . END=7650 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1034 -20_10037292_10066351 7651 . C . . END=7657 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 7658 . T . . END=7658 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,981 -20_10037292_10066351 7659 . G . . END=7665 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 7666 . A . . END=7667 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 7668 . C . . END=7668 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 7669 . C . . END=7679 GT:DP:GQ:MIN_DP:PL 0/0:31:82:29:0,82,996 -20_10037292_10066351 7680 . A . . END=7680 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,895 -20_10037292_10066351 7681 . C . . END=7684 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 7685 . G . . END=7685 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,993 -20_10037292_10066351 7686 . T . . END=7686 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 7687 . T . . END=7687 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1008 -20_10037292_10066351 7688 . A . . END=7690 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 7691 . C . . END=7691 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,974 -20_10037292_10066351 7692 . C . . END=7695 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,936 -20_10037292_10066351 7696 . T . . END=7696 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,929 -20_10037292_10066351 7697 . A . . END=7705 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,990 -20_10037292_10066351 7706 . C . . END=7706 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,895 -20_10037292_10066351 7707 . A . . END=7708 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 7709 . T . . END=7709 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,937 -20_10037292_10066351 7710 . C . . END=7712 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 7713 . T . . END=7713 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1093 -20_10037292_10066351 7714 . A . . END=7714 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7715 . C . . END=7715 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1058 -20_10037292_10066351 7716 . A . . END=7718 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7719 . C . . END=7719 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1091 -20_10037292_10066351 7720 . C . . END=7723 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 7724 . A . . END=7724 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1138 -20_10037292_10066351 7725 . C . . END=7730 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 7731 . A . . END=7742 GT:DP:GQ:MIN_DP:PL 0/0:36:90:32:0,90,1350 -20_10037292_10066351 7743 . A . . END=7744 GT:DP:GQ:MIN_DP:PL 0/0:33:84:32:0,84,1260 -20_10037292_10066351 7745 . A . . END=7748 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1131 -20_10037292_10066351 7749 . T . . END=7751 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 7752 . C . . END=7752 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1118 -20_10037292_10066351 7753 . T . . END=7753 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 7754 . C . . END=7754 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1032 -20_10037292_10066351 7755 . C . . END=7763 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 7764 . T . . END=7764 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1019 -20_10037292_10066351 7765 . T . . END=7769 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 7770 . C . . END=7774 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7775 . A . . END=7775 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1053 -20_10037292_10066351 7776 . A . . END=7780 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 7781 . A . . END=7785 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1115 -20_10037292_10066351 7786 . G T, 1043.06 . DP=35;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=126000,35 GT:AD:DP:GQ:PL:SB 1/1:0,34,0:34:99:1057,102,0,1057,102,1057:0,0,19,15 -20_10037292_10066351 7787 . C . . END=7795 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 7796 . A . . END=7796 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1024 -20_10037292_10066351 7797 . A . . END=7798 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 7799 . T . . END=7799 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1065 -20_10037292_10066351 7800 . C . . END=7812 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,102,1061 -20_10037292_10066351 7813 . T . . END=7813 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,1099 -20_10037292_10066351 7814 . T . . END=7859 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1254 -20_10037292_10066351 7860 . G . . END=7860 GT:DP:GQ:MIN_DP:PL 0/0:42:95:42:0,95,1293 -20_10037292_10066351 7861 . A . . END=7863 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,108,1620 -20_10037292_10066351 7864 . G . . END=7864 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1148 -20_10037292_10066351 7865 . C . . END=7873 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 7874 . G . . END=7874 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1195 -20_10037292_10066351 7875 . A . . END=7879 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 7880 . T . . END=7887 GT:DP:GQ:MIN_DP:PL 0/0:35:93:33:0,93,1395 -20_10037292_10066351 7888 . A . . END=7888 GT:DP:GQ:MIN_DP:PL 0/0:34:74:34:0,74,1071 -20_10037292_10066351 7889 . A . . END=7894 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 7895 . C . . END=7895 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1094 -20_10037292_10066351 7896 . C . . END=7909 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1011 -20_10037292_10066351 7910 . G . . END=7918 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,1215 -20_10037292_10066351 7919 . G . . END=7919 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,968 -20_10037292_10066351 7920 . T . . END=7926 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 7927 . A . . END=7929 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1003 -20_10037292_10066351 7930 . G . . END=7930 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,970 -20_10037292_10066351 7931 . A . . END=7933 GT:DP:GQ:MIN_DP:PL 0/0:34:90:30:0,90,986 -20_10037292_10066351 7934 . A . . END=7951 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1485 -20_10037292_10066351 7952 . T . . END=7952 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1244 -20_10037292_10066351 7953 . G . . END=7963 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1172 -20_10037292_10066351 7964 . T . . END=7964 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 7965 . T . . END=7967 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 7968 . C . . END=7968 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1440 -20_10037292_10066351 7969 . T . . END=7975 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 7976 . T . . END=7976 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1161 -20_10037292_10066351 7977 . A . . END=7986 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,101,1160 -20_10037292_10066351 7987 . T . . END=7987 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1081 -20_10037292_10066351 7988 . G . . END=7990 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 7991 . G . . END=7991 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1134 -20_10037292_10066351 7992 . A . . END=8011 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1155 -20_10037292_10066351 8012 . A . . END=8012 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1234 -20_10037292_10066351 8013 . A . . END=8079 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,99,1221 -20_10037292_10066351 8080 . C . . END=8083 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 8084 . G . . END=8086 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 8087 . A . . END=8093 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8094 . A . . END=8096 GT:DP:GQ:MIN_DP:PL 0/0:34:81:34:0,81,992 -20_10037292_10066351 8097 . A . . END=8098 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 8099 . T . . END=8099 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,989 -20_10037292_10066351 8100 . A . . END=8102 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1064 -20_10037292_10066351 8103 . A . . END=8103 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1037 -20_10037292_10066351 8104 . A . . END=8104 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1037 -20_10037292_10066351 8105 . A . . END=8105 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1022 -20_10037292_10066351 8106 . T . . END=8106 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8107 . G . . END=8109 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1018 -20_10037292_10066351 8110 . C . . END=8117 GT:DP:GQ:MIN_DP:PL 0/0:33:75:28:0,75,1125 -20_10037292_10066351 8118 . A . . END=8121 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 8122 . G . . END=8130 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,945 -20_10037292_10066351 8131 . A . . END=8131 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8132 . C . . END=8132 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,970 -20_10037292_10066351 8133 . A . . END=8135 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,954 -20_10037292_10066351 8136 . C . . END=8140 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 8141 . G . . END=8141 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8142 . A . . END=8144 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8145 . T . . END=8150 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8151 . A . . END=8156 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8157 . C . . END=8157 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 8158 . C . . END=8180 GT:DP:GQ:MIN_DP:PL 0/0:28:70:26:0,70,854 -20_10037292_10066351 8181 . A . . END=8181 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,812 -20_10037292_10066351 8182 . T . . END=8204 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,730 -20_10037292_10066351 8205 . G . . END=8205 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,702 -20_10037292_10066351 8206 . T . . END=8206 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8207 . C . . END=8207 GT:DP:GQ:MIN_DP:PL 0/0:26:62:26:0,62,793 -20_10037292_10066351 8208 . C . . END=8209 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8210 . T . . END=8210 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,868 -20_10037292_10066351 8211 . T . . END=8216 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 8217 . A . . END=8223 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,854 -20_10037292_10066351 8224 . T . . END=8229 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8230 . A . . END=8235 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1055 -20_10037292_10066351 8236 . G . . END=8236 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,999 -20_10037292_10066351 8237 . C . . END=8240 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8241 . A . . END=8241 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1044 -20_10037292_10066351 8242 . C . . END=8247 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 8248 . T . . END=8250 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1103 -20_10037292_10066351 8251 . C . . END=8251 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1026 -20_10037292_10066351 8252 . C . . END=8258 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,102,1121 -20_10037292_10066351 8259 . T . . END=8259 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1226 -20_10037292_10066351 8260 . T . . END=8261 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 8262 . T . . END=8269 GT:DP:GQ:MIN_DP:PL 0/0:38:93:36:0,93,1395 -20_10037292_10066351 8270 . C . . END=8270 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1122 -20_10037292_10066351 8271 . T . . END=8272 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 8273 . T . . END=8274 GT:DP:GQ:MIN_DP:PL 0/0:34:80:34:0,80,1002 -20_10037292_10066351 8275 . T . . END=8276 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,1073 -20_10037292_10066351 8277 . G . . END=8277 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,1011 -20_10037292_10066351 8278 . C . . END=8278 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1007 -20_10037292_10066351 8279 . C . . END=8279 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,970 -20_10037292_10066351 8280 . A . . END=8280 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1088 -20_10037292_10066351 8281 . T . . END=8282 GT:DP:GQ:MIN_DP:PL 0/0:34:82:33:0,82,1000 -20_10037292_10066351 8283 . C . . END=8285 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1075 -20_10037292_10066351 8286 . T . . END=8286 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1030 -20_10037292_10066351 8287 . T . . END=8292 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8293 . C . . END=8293 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1030 -20_10037292_10066351 8294 . A . . END=8296 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8297 . A . . END=8297 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 8298 . C . . END=8298 GT:DP:GQ:MIN_DP:PL 0/0:36:74:36:0,74,1031 -20_10037292_10066351 8299 . T . . END=8299 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1109 -20_10037292_10066351 8300 . C . . END=8305 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1167 -20_10037292_10066351 8306 . A . . END=8307 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1113 -20_10037292_10066351 8308 . C . . END=8308 GT:DP:GQ:MIN_DP:PL 0/0:34:72:34:0,72,991 -20_10037292_10066351 8309 . A . . END=8310 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8311 . C . . END=8311 GT:DP:GQ:MIN_DP:PL 0/0:34:70:34:0,70,951 -20_10037292_10066351 8312 . A . . END=8314 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8315 . C . . END=8332 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,990 -20_10037292_10066351 8333 . T . . END=8333 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1016 -20_10037292_10066351 8334 . A . . END=8335 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8336 . G . . END=8336 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1037 -20_10037292_10066351 8337 . A . . END=8337 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 8338 . C . . END=8338 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1023 -20_10037292_10066351 8339 . T . . END=8339 GT:DP:GQ:MIN_DP:PL 0/0:36:69:36:0,69,1050 -20_10037292_10066351 8340 . T . . END=8340 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1102 -20_10037292_10066351 8341 . A . . END=8341 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8342 . G . . END=8342 GT:DP:GQ:MIN_DP:PL 0/0:36:88:36:0,88,1074 -20_10037292_10066351 8343 . A . . END=8349 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,117,1755 -20_10037292_10066351 8350 . G C, 1162.06 . DP=39;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=140400,39 GT:AD:DP:GQ:PL:SB 1/1:0,39,0:39:99:1176,115,0,1176,115,1176:0,0,16,23 -20_10037292_10066351 8351 . A . . END=8355 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,114,1710 -20_10037292_10066351 8356 . T . . END=8356 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1267 -20_10037292_10066351 8357 . T . . END=8357 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1620 -20_10037292_10066351 8358 . A . . END=8358 GT:DP:GQ:MIN_DP:PL 0/0:41:94:41:0,94,1232 -20_10037292_10066351 8359 . A . . END=8365 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,99,1210 -20_10037292_10066351 8366 . A . . END=8367 GT:DP:GQ:MIN_DP:PL 0/0:38:96:37:0,96,1440 -20_10037292_10066351 8368 . T . . END=8368 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 8369 . T . . END=8369 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1156 -20_10037292_10066351 8370 . C . . END=8378 GT:DP:GQ:MIN_DP:PL 0/0:39:99:34:0,99,1485 -20_10037292_10066351 8379 . G . . END=8388 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8389 . G . . END=8394 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 8395 . A . . END=8396 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8397 . G . . END=8400 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 8401 . A . . END=8401 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,920 -20_10037292_10066351 8402 . A . . END=8408 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,947 -20_10037292_10066351 8409 . C . . END=8425 GT:DP:GQ:MIN_DP:PL 0/0:29:72:27:0,72,1080 -20_10037292_10066351 8426 . C . . END=8426 GT:DP:GQ:MIN_DP:PL 0/0:27:36:27:0,36,772 -20_10037292_10066351 8427 . T . . END=8428 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 8429 . T . . END=8438 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 8439 . G . . END=8439 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,935 -20_10037292_10066351 8440 . C . . END=8440 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8441 . T . . END=8458 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,938 -20_10037292_10066351 8459 . G . . END=8483 GT:DP:GQ:MIN_DP:PL 0/0:40:99:35:0,102,1192 -20_10037292_10066351 8484 . T . . END=8501 GT:DP:GQ:MIN_DP:PL 0/0:38:90:30:0,90,944 -20_10037292_10066351 8502 . A . . END=8512 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8513 . G . . END=8513 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,919 -20_10037292_10066351 8514 . A . . END=8521 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,956 -20_10037292_10066351 8522 . A . . END=8529 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,934 -20_10037292_10066351 8530 . C . . END=8530 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,911 -20_10037292_10066351 8531 . C . . END=8537 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,980 -20_10037292_10066351 8538 . A . . END=8549 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 8550 . A . . END=8556 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 8557 . A . . END=8576 GT:DP:GQ:MIN_DP:PL 0/0:36:99:33:0,99,1007 -20_10037292_10066351 8577 . G . . END=8581 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1087 -20_10037292_10066351 8582 . C . . END=8584 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8585 . T . . END=8587 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 8588 . C . . END=8591 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 8592 . T . . END=8592 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1049 -20_10037292_10066351 8593 . G . . END=8595 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1040 -20_10037292_10066351 8596 . C . . END=8599 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 8600 . T . . END=8606 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,1260 -20_10037292_10066351 8607 . C . . END=8609 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,1170 -20_10037292_10066351 8610 . G . . END=8611 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8612 . T . . END=8613 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8614 . G . . END=8620 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8621 . C . . END=8621 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,915 -20_10037292_10066351 8622 . A . . END=8623 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,864 -20_10037292_10066351 8624 . T . . END=8624 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,872 -20_10037292_10066351 8625 . G . . END=8633 GT:DP:GQ:MIN_DP:PL 0/0:30:84:28:0,84,928 -20_10037292_10066351 8634 . T . . END=8634 GT:DP:GQ:MIN_DP:PL 0/0:28:63:28:0,63,877 -20_10037292_10066351 8635 . G . . END=8637 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8638 . T . . END=8638 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,847 -20_10037292_10066351 8639 . C . . END=8644 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8645 . T . . END=8645 GT:DP:GQ:MIN_DP:PL 0/0:28:53:28:0,53,770 -20_10037292_10066351 8646 . C . . END=8646 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,950 -20_10037292_10066351 8647 . T . . END=8668 GT:DP:GQ:MIN_DP:PL 0/0:33:90:30:0,90,922 -20_10037292_10066351 8669 . C . . END=8672 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8673 . A . . END=8673 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8674 . G . . END=8674 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1037 -20_10037292_10066351 8675 . G . . END=8676 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8677 . C . . END=8678 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 8679 . C . . END=8683 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 8684 . T . . END=8684 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1090 -20_10037292_10066351 8685 . T . . END=8702 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1065 -20_10037292_10066351 8703 . T . . END=8703 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8704 . T . . END=8704 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1041 -20_10037292_10066351 8705 . T . . END=8720 GT:DP:GQ:MIN_DP:PL 0/0:35:90:33:0,90,1064 -20_10037292_10066351 8721 . A . . END=8725 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8726 . A . . END=8728 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8729 . A . . END=8736 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,928 -20_10037292_10066351 8737 . T . . END=8741 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8742 . A . . END=8742 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,952 -20_10037292_10066351 8743 . A . . END=8745 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,980 -20_10037292_10066351 8746 . C . . END=8746 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,822 -20_10037292_10066351 8747 . A . . END=8747 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,986 -20_10037292_10066351 8748 . C . . END=8749 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 8750 . A . . END=8751 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,979 -20_10037292_10066351 8752 . A . . END=8753 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8754 . T . . END=8754 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,929 -20_10037292_10066351 8755 . G . . END=8757 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8758 . A . . END=8758 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1005 -20_10037292_10066351 8759 . C . . END=8770 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 8771 . T . . END=8771 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,819 -20_10037292_10066351 8772 . G . . END=8773 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8774 . G . . END=8774 GT:DP:GQ:MIN_DP:PL 0/0:33:71:33:0,71,962 -20_10037292_10066351 8775 . C . . END=8775 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8776 . T . . END=8776 GT:DP:GQ:MIN_DP:PL 0/0:33:52:33:0,52,865 -20_10037292_10066351 8777 . C . . END=8778 GT:DP:GQ:MIN_DP:PL 0/0:34:82:33:0,82,789 -20_10037292_10066351 8779 . C . . END=8779 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,883 -20_10037292_10066351 8780 . A . . END=8781 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,114,1174 -20_10037292_10066351 8782 . G . . END=8782 GT:DP:GQ:MIN_DP:PL 0/0:37:33:37:0,33,916 -20_10037292_10066351 8783 . A . . END=8791 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1182 -20_10037292_10066351 8792 . G . . END=8792 GT:DP:GQ:MIN_DP:PL 0/0:39:78:39:0,78,1074 -20_10037292_10066351 8793 . G . . END=8800 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1039 -20_10037292_10066351 8801 . T . . END=8801 GT:DP:GQ:MIN_DP:PL 0/0:40:81:40:0,81,1090 -20_10037292_10066351 8802 . T . . END=8802 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,106,1067 -20_10037292_10066351 8803 . C . . END=8803 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,984 -20_10037292_10066351 8804 . C . . END=8804 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,102,1041 -20_10037292_10066351 8805 . C . . END=8805 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,986 -20_10037292_10066351 8806 . C . . END=8806 GT:DP:GQ:MIN_DP:PL 0/0:38:79:38:0,79,1019 -20_10037292_10066351 8807 . A . . END=8813 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,111,1665 -20_10037292_10066351 8814 . G . . END=8814 GT:DP:GQ:MIN_DP:PL 0/0:40:76:40:0,76,1133 -20_10037292_10066351 8815 . A . . END=8816 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 8817 . T . . END=8817 GT:DP:GQ:MIN_DP:PL 0/0:39:39:39:0,39,868 -20_10037292_10066351 8818 . T . . END=8826 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1002 -20_10037292_10066351 8827 . T . . END=8827 GT:DP:GQ:MIN_DP:PL 0/0:38:75:38:0,75,1016 -20_10037292_10066351 8828 . G . . END=8828 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 8829 . G . . END=8831 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 8832 . A . . END=8834 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 8835 . C . . END=8835 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,892 -20_10037292_10066351 8836 . A . . END=8836 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8837 . G . . END=8837 GT:DP:GQ:MIN_DP:PL 0/0:35:61:35:0,61,962 -20_10037292_10066351 8838 . A . . END=8841 GT:DP:GQ:MIN_DP:PL 0/0:35:96:33:0,96,1440 -20_10037292_10066351 8842 . A . . END=8843 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 8844 . A . . END=8844 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1120 -20_10037292_10066351 8845 . A . . END=8845 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8846 . G . . END=8846 GT:DP:GQ:MIN_DP:PL 0/0:36:74:36:0,74,1003 -20_10037292_10066351 8847 . G . . END=8847 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1017 -20_10037292_10066351 8848 . G . . END=8848 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1030 -20_10037292_10066351 8849 . A . . END=8849 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1039 -20_10037292_10066351 8850 . A . . END=8856 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 8857 . A . . END=8857 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1039 -20_10037292_10066351 8858 . G . . END=8858 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,999 -20_10037292_10066351 8859 . G . . END=8860 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8861 . A . . END=8861 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1118 -20_10037292_10066351 8862 . G . . END=8862 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 8863 . G . . END=8863 GT:DP:GQ:MIN_DP:PL 0/0:37:91:37:0,91,1058 -20_10037292_10066351 8864 . G . . END=8864 GT:DP:GQ:MIN_DP:PL 0/0:37:85:37:0,85,1033 -20_10037292_10066351 8865 . G . . END=8869 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1530 -20_10037292_10066351 8870 . G . . END=8870 GT:DP:GQ:MIN_DP:PL 0/0:38:78:38:0,78,1017 -20_10037292_10066351 8871 . G . . END=8871 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1039 -20_10037292_10066351 8872 . A . . END=8880 GT:DP:GQ:MIN_DP:PL 0/0:37:93:36:0,93,1054 -20_10037292_10066351 8881 . A . . END=8881 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1054 -20_10037292_10066351 8882 . A . . END=8882 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 8883 . A . . END=8883 GT:DP:GQ:MIN_DP:PL 0/0:37:87:37:0,87,1305 -20_10037292_10066351 8884 . G . . END=8884 GT:DP:GQ:MIN_DP:PL 0/0:36:77:36:0,77,1086 -20_10037292_10066351 8885 . A . . END=8885 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,966 -20_10037292_10066351 8886 . AAGAAAGAAAG A, 1268.03 . DP=34;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=122400,34 GT:AD:DP:GQ:PL:SB 1/1:0,29,0:29:88:1282,88,0,1282,88,1282:0,0,17,12 -20_10037292_10066351 8897 . A . . END=8903 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 -20_10037292_10066351 8904 . A . . END=8904 GT:DP:GQ:MIN_DP:PL 0/0:35:0:35:0,0,695 -20_10037292_10066351 8905 . A . . END=8905 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 8906 . G . . END=8906 GT:DP:GQ:MIN_DP:PL 0/0:35:0:35:0,0,689 -20_10037292_10066351 8907 . A . . END=8907 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8908 . G . . END=8908 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1032 -20_10037292_10066351 8909 . A . . END=8911 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8912 . G . . END=8912 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,963 -20_10037292_10066351 8913 . A . . END=8916 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 8917 . A . . END=8917 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,870 -20_10037292_10066351 8918 . G . . END=8918 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,892 -20_10037292_10066351 8919 . A . . END=8919 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 8920 . A . . END=8920 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,867 -20_10037292_10066351 8921 . A . . END=8921 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8922 . G . . END=8922 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,925 -20_10037292_10066351 8923 . A . . END=8923 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 8924 . G . . END=8924 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,884 -20_10037292_10066351 8925 . G . . END=8925 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,925 -20_10037292_10066351 8926 . A . . END=8926 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,827 -20_10037292_10066351 8927 . A . . END=8928 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 8929 . G . . END=8929 GT:DP:GQ:MIN_DP:PL 0/0:32:33:32:0,33,853 -20_10037292_10066351 8930 . A . . END=8931 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,1215 -20_10037292_10066351 8932 . A . . END=8932 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8933 . G . . END=8933 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,979 -20_10037292_10066351 8934 . A . . END=8937 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 8938 . A . . END=8938 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,1170 -20_10037292_10066351 8939 . G . . END=8939 GT:DP:GQ:MIN_DP:PL 0/0:35:42:35:0,42,927 -20_10037292_10066351 8940 . A . . END=8941 GT:DP:GQ:MIN_DP:PL 0/0:34:81:32:0,81,1215 -20_10037292_10066351 8942 . A . . END=8944 GT:DP:GQ:MIN_DP:PL 0/0:34:78:33:0,78,1170 -20_10037292_10066351 8945 . G . . END=8945 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,909 -20_10037292_10066351 8946 . A . . END=8948 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,882 -20_10037292_10066351 8949 . G . . END=8952 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 -20_10037292_10066351 8953 . G . . END=8953 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,878 -20_10037292_10066351 8954 . A . . END=8954 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8955 . G . . END=8955 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,881 -20_10037292_10066351 8956 . A . . END=8961 GT:DP:GQ:MIN_DP:PL 0/0:32:80:30:0,80,916 -20_10037292_10066351 8962 . A . . END=8963 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,869 -20_10037292_10066351 8964 . A . . END=8964 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8965 . G . . END=8965 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,792 -20_10037292_10066351 8966 . A . . END=8967 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,872 -20_10037292_10066351 8968 . G . . END=8968 GT:DP:GQ:MIN_DP:PL 0/0:33:27:33:0,27,752 -20_10037292_10066351 8969 . G . . END=8974 GT:DP:GQ:MIN_DP:PL 0/0:34:83:32:0,83,944 -20_10037292_10066351 8975 . G . . END=8975 GT:DP:GQ:MIN_DP:PL 0/0:34:70:34:0,70,857 -20_10037292_10066351 8976 . A . . END=8976 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8977 . G . . END=8977 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,895 -20_10037292_10066351 8978 . A . . END=8980 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8981 . G . . END=8981 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,921 -20_10037292_10066351 8982 . A . . END=8984 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8985 . A . . END=8993 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 8994 . A . . END=8994 GT:DP:GQ:MIN_DP:PL 0/0:31:68:31:0,68,872 -20_10037292_10066351 8995 . G . . END=8995 GT:DP:GQ:MIN_DP:PL 0/0:31:28:31:0,28,772 -20_10037292_10066351 8996 . A . . END=8996 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8997 . G . . END=8997 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,833 -20_10037292_10066351 8998 . A . . END=9007 GT:DP:GQ:MIN_DP:PL 0/0:33:81:30:0,81,958 -20_10037292_10066351 9008 . G . . END=9008 GT:DP:GQ:MIN_DP:PL 0/0:34:73:34:0,73,965 -20_10037292_10066351 9009 . A . . END=9010 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 9011 . G . . END=9011 GT:DP:GQ:MIN_DP:PL 0/0:34:66:34:0,66,929 -20_10037292_10066351 9012 . G . . END=9013 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,908 -20_10037292_10066351 9014 . A . . END=9014 GT:DP:GQ:MIN_DP:PL 0/0:33:70:33:0,70,956 -20_10037292_10066351 9015 . G . . END=9015 GT:DP:GQ:MIN_DP:PL 0/0:32:13:32:0,13,731 -20_10037292_10066351 9016 . G . . END=9016 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,884 -20_10037292_10066351 9017 . A . . END=9017 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1007 -20_10037292_10066351 9018 . A . . END=9018 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9019 . G . . END=9019 GT:DP:GQ:MIN_DP:PL 0/0:39:69:39:0,69,1010 -20_10037292_10066351 9020 . A . . END=9020 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 9021 . A . . END=9021 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1070 -20_10037292_10066351 9022 . A . . END=9024 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1080 -20_10037292_10066351 9025 . T . . END=9025 GT:DP:GQ:MIN_DP:PL 0/0:37:0:37:0,0,654 -20_10037292_10066351 9026 . G . . END=9026 GT:DP:GQ:MIN_DP:PL 0/0:37:83:37:0,83,1047 -20_10037292_10066351 9027 . A . . END=9028 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1620 -20_10037292_10066351 9029 . G . . END=9029 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1046 -20_10037292_10066351 9030 . G . . END=9030 GT:DP:GQ:MIN_DP:PL 0/0:38:56:38:0,56,999 -20_10037292_10066351 9031 . G . . END=9031 GT:DP:GQ:MIN_DP:PL 0/0:38:70:38:0,70,1004 -20_10037292_10066351 9032 . A . . END=9032 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9033 . G . . END=9033 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1083 -20_10037292_10066351 9034 . G . . END=9034 GT:DP:GQ:MIN_DP:PL 0/0:38:25:38:0,25,908 -20_10037292_10066351 9035 . A . . END=9035 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1012 -20_10037292_10066351 9036 . A . . END=9036 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9037 . G . . END=9037 GT:DP:GQ:MIN_DP:PL 0/0:38:71:38:0,71,1040 -20_10037292_10066351 9038 . G . . END=9038 GT:DP:GQ:MIN_DP:PL 0/0:36:41:36:0,41,937 -20_10037292_10066351 9039 . A . . END=9042 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 9043 . A . . END=9043 GT:DP:GQ:MIN_DP:PL 0/0:36:83:36:0,83,1090 -20_10037292_10066351 9044 . G . . END=9044 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 9045 . G . . END=9045 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1010 -20_10037292_10066351 9046 . A . . END=9050 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 9051 . G . . END=9051 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,1041 -20_10037292_10066351 9052 . G . . END=9052 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1030 -20_10037292_10066351 9053 . A . . END=9053 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 9054 . A . . END=9054 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1075 -20_10037292_10066351 9055 . G . . END=9060 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,101,974 -20_10037292_10066351 9061 . A . . END=9068 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 9069 . G . . END=9069 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1056 -20_10037292_10066351 9070 . A . . END=9070 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 9071 . A . . END=9071 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 9072 . G . . END=9073 GT:DP:GQ:MIN_DP:PL 0/0:37:64:37:0,64,1071 -20_10037292_10066351 9074 . A . . END=9074 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9075 . A . . END=9076 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,106,1209 -20_10037292_10066351 9077 . A . . END=9082 GT:DP:GQ:MIN_DP:PL 0/0:38:90:36:0,90,1214 -20_10037292_10066351 9083 . G . . END=9083 GT:DP:GQ:MIN_DP:PL 0/0:37:86:37:0,86,1135 -20_10037292_10066351 9084 . G . . END=9084 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 9085 . G . . END=9085 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1148 -20_10037292_10066351 9086 . G . . END=9088 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 9089 . G . . END=9097 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,934 -20_10037292_10066351 9098 . G . . END=9098 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,971 -20_10037292_10066351 9099 . G . . END=9101 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,981 -20_10037292_10066351 9102 . T . . END=9102 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,847 -20_10037292_10066351 9103 . A . . END=9103 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,860 -20_10037292_10066351 9104 . A . . END=9104 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 9105 . A . . END=9105 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 9106 . G . . END=9106 GT:DP:GQ:MIN_DP:PL 0/0:29:64:29:0,64,878 -20_10037292_10066351 9107 . A . . END=9107 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 9108 . A . . END=9108 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9109 . A . . END=9109 GT:DP:GQ:MIN_DP:PL 0/0:31:71:31:0,71,936 -20_10037292_10066351 9110 . G . . END=9110 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,914 -20_10037292_10066351 9111 . A . . END=9112 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9113 . G . . END=9118 GT:DP:GQ:MIN_DP:PL 0/0:31:72:31:0,72,1080 -20_10037292_10066351 9119 . G . . END=9119 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,873 -20_10037292_10066351 9120 . A . . END=9120 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 9121 . T . . END=9121 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,869 -20_10037292_10066351 9122 . G . . END=9122 GT:DP:GQ:MIN_DP:PL 0/0:28:52:28:0,52,788 -20_10037292_10066351 9123 . G . . END=9123 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,830 -20_10037292_10066351 9124 . A . . END=9124 GT:DP:GQ:MIN_DP:PL 0/0:28:51:28:0,51,802 -20_10037292_10066351 9125 . G . . END=9125 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,799 -20_10037292_10066351 9126 . A . . END=9126 GT:DP:GQ:MIN_DP:PL 0/0:27:58:27:0,58,789 -20_10037292_10066351 9127 . A . . END=9127 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 9128 . G . . END=9128 GT:DP:GQ:MIN_DP:PL 0/0:27:53:27:0,53,781 -20_10037292_10066351 9129 . A . . END=9135 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,809 -20_10037292_10066351 9136 . A . . END=9136 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,796 -20_10037292_10066351 9137 . C . . END=9140 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 9141 . A . . END=9142 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 9143 . A . . END=9143 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,887 -20_10037292_10066351 9144 . A . . END=9145 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9146 . T . . END=9146 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,817 -20_10037292_10066351 9147 . G . . END=9147 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,824 -20_10037292_10066351 9148 . G . . END=9148 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,800 -20_10037292_10066351 9149 . C . . END=9152 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,822 -20_10037292_10066351 9153 . T . . END=9153 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,914 -20_10037292_10066351 9154 . A . . END=9154 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,804 -20_10037292_10066351 9155 . C . . END=9158 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,889 -20_10037292_10066351 9159 . C . . END=9163 GT:DP:GQ:MIN_DP:PL 0/0:34:81:27:0,81,827 -20_10037292_10066351 9164 . C . . END=9167 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1016 -20_10037292_10066351 9168 . A . . END=9168 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 9169 . C . . END=9175 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9176 . A . . END=9199 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,981 -20_10037292_10066351 9200 . T . . END=9200 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1180 -20_10037292_10066351 9201 . T . . END=9201 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,111,1221 -20_10037292_10066351 9202 . T . . END=9202 GT:DP:GQ:MIN_DP:PL 0/0:42:90:42:0,90,1135 -20_10037292_10066351 9203 . C . . END=9225 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,100,1080 -20_10037292_10066351 9226 . G . . END=9226 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1056 -20_10037292_10066351 9227 . C . . END=9227 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9228 . T . . END=9228 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1056 -20_10037292_10066351 9229 . C . . END=9229 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9230 . T . . END=9230 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1055 -20_10037292_10066351 9231 . C . . END=9236 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,104,1030 -20_10037292_10066351 9237 . G . . END=9237 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1042 -20_10037292_10066351 9238 . C . . END=9239 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1017 -20_10037292_10066351 9240 . A . . END=9242 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 9243 . T . . END=9244 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1084 -20_10037292_10066351 9245 . A G, 26.64 . BaseQRankSum=-1.133;DP=35;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=126000,35;ReadPosRankSum=1.071 GT:AD:DP:GQ:PL:SB 0/1:29,5,0:34:34:34,0,814,120,828,948:11,18,1,4 -20_10037292_10066351 9246 . T . . END=9246 GT:DP:GQ:MIN_DP:PL 0/0:37:83:37:0,83,1071 -20_10037292_10066351 9247 . T . . END=9262 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1084 -20_10037292_10066351 9263 . G . . END=9265 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1018 -20_10037292_10066351 9266 . T . . END=9266 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,111,1161 -20_10037292_10066351 9267 . G . . END=9267 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1120 -20_10037292_10066351 9268 . A . . END=9268 GT:DP:GQ:MIN_DP:PL 0/0:38:73:38:0,73,909 -20_10037292_10066351 9269 . C . . END=9350 GT:DP:GQ:MIN_DP:PL 0/0:45:99:38:0,105,1281 -20_10037292_10066351 9351 . A . . END=9351 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1158 -20_10037292_10066351 9352 . T . . END=9355 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,105,1575 -20_10037292_10066351 9356 . C . . END=9356 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1127 -20_10037292_10066351 9357 . A . . END=9358 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1169 -20_10037292_10066351 9359 . A . . END=9359 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1110 -20_10037292_10066351 9360 . C . . END=9361 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1087 -20_10037292_10066351 9362 . C . . END=9362 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1186 -20_10037292_10066351 9363 . T . . END=9406 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,104,1220 -20_10037292_10066351 9407 . G . . END=9407 GT:DP:GQ:MIN_DP:PL 0/0:45:93:45:0,93,1366 -20_10037292_10066351 9408 . C . . END=9414 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,105,1575 -20_10037292_10066351 9415 . T . . END=9425 GT:DP:GQ:MIN_DP:PL 0/0:39:90:35:0,90,1068 -20_10037292_10066351 9426 . T . . END=9427 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,996 -20_10037292_10066351 9428 . A . . END=9428 GT:DP:GQ:MIN_DP:PL 0/0:32:71:32:0,71,957 -20_10037292_10066351 9429 . C . . END=9439 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,877 -20_10037292_10066351 9440 . T . . END=9440 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9441 . T . . END=9452 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 9453 . A . . END=9454 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,870 -20_10037292_10066351 9455 . G . . END=9457 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 9458 . A . . END=9468 GT:DP:GQ:MIN_DP:PL 0/0:30:72:29:0,72,898 -20_10037292_10066351 9469 . T . . END=9469 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,791 -20_10037292_10066351 9470 . C . . END=9471 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 9472 . G . . END=9488 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,965 -20_10037292_10066351 9489 . C . . END=9489 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,962 -20_10037292_10066351 9490 . C . . END=9491 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,946 -20_10037292_10066351 9492 . A . . END=9493 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,1034 -20_10037292_10066351 9494 . A . . END=9494 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1040 -20_10037292_10066351 9495 . T . . END=9495 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9496 . A . . END=9496 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 9497 . T . . END=9497 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1047 -20_10037292_10066351 9498 . C . . END=9500 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 9501 . C . . END=9505 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9506 . C . . END=9507 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 9508 . T . . END=9508 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9509 . G . . END=9512 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,1305 -20_10037292_10066351 9513 . C . . END=9513 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 9514 . C . . END=9518 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 9519 . G . . END=9519 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,915 -20_10037292_10066351 9520 . C . . END=9521 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9522 . C . . END=9525 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 9526 . C . . END=9528 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 9529 . A . . END=9529 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,772 -20_10037292_10066351 9530 . C . . END=9533 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 9534 . A . . END=9534 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,826 -20_10037292_10066351 9535 . A . . END=9544 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9545 . A . . END=9546 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,800 -20_10037292_10066351 9547 . T . . END=9549 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,954 -20_10037292_10066351 9550 . A . . END=9551 GT:DP:GQ:MIN_DP:PL 0/0:32:70:31:0,70,887 -20_10037292_10066351 9552 . C . . END=9552 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 9553 . T . . END=9553 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,925 -20_10037292_10066351 9554 . C . . END=9556 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9557 . A . . END=9558 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,839 -20_10037292_10066351 9559 . A . . END=9562 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,959 -20_10037292_10066351 9563 . T . . END=9563 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,1004 -20_10037292_10066351 9564 . T . . END=9564 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1041 -20_10037292_10066351 9565 . G . . END=9565 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,927 -20_10037292_10066351 9566 . T . . END=9567 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9568 . A . . END=9568 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,887 -20_10037292_10066351 9569 . C . . END=9569 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9570 . T . . END=9570 GT:DP:GQ:MIN_DP:PL 0/0:33:54:33:0,54,838 -20_10037292_10066351 9571 . C . . END=9571 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9572 . T . . END=9572 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,963 -20_10037292_10066351 9573 . T . . END=9574 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9575 . C . . END=9575 GT:DP:GQ:MIN_DP:PL 0/0:33:88:33:0,88,1021 -20_10037292_10066351 9576 . T . . END=9576 GT:DP:GQ:MIN_DP:PL 0/0:34:54:34:0,54,906 -20_10037292_10066351 9577 . C . . END=9578 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9579 . T . . END=9579 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,994 -20_10037292_10066351 9580 . A . . END=9580 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,872 -20_10037292_10066351 9581 . C . . END=9587 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 9588 . C . . END=9589 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,862 -20_10037292_10066351 9590 . C . . END=9593 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9594 . T . . END=9607 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,956 -20_10037292_10066351 9608 . A . . END=9608 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1158 -20_10037292_10066351 9609 . C . . END=9646 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,107,1228 -20_10037292_10066351 9647 . G . . END=9647 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1214 -20_10037292_10066351 9648 . A . . END=9650 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,114,1710 -20_10037292_10066351 9651 . T . . END=9651 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1301 -20_10037292_10066351 9652 . G . . END=9659 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,114,1710 -20_10037292_10066351 9660 . A . . END=9660 GT:DP:GQ:MIN_DP:PL 0/0:40:98:40:0,98,1230 -20_10037292_10066351 9661 . T . . END=9687 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,102,1188 -20_10037292_10066351 9688 . A . . END=9688 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1182 -20_10037292_10066351 9689 . C . . END=9700 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,117,1755 -20_10037292_10066351 9701 . A . . END=9701 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1221 -20_10037292_10066351 9702 . C . . END=9711 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,107,1235 -20_10037292_10066351 9712 . C . . END=9712 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1180 -20_10037292_10066351 9713 . A . . END=9736 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1195 -20_10037292_10066351 9737 . T . . END=9745 GT:DP:GQ:MIN_DP:PL 0/0:39:90:37:0,90,1350 -20_10037292_10066351 9746 . T . . END=9748 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 9749 . C . . END=9753 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 9754 . A . . END=9754 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,887 -20_10037292_10066351 9755 . A . . END=9755 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9756 . T . . END=9757 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 9758 . A . . END=9758 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 9759 . A . . END=9761 GT:DP:GQ:MIN_DP:PL 0/0:33:84:32:0,84,1260 -20_10037292_10066351 9762 . T . . END=9762 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,1064 -20_10037292_10066351 9763 . A . . END=9765 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9766 . T . . END=9770 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1058 -20_10037292_10066351 9771 . A . . END=9771 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9772 . A . . END=9772 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1019 -20_10037292_10066351 9773 . T . . END=9775 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 9776 . C . . END=9777 GT:DP:GQ:MIN_DP:PL 0/0:36:77:35:0,77,1058 -20_10037292_10066351 9778 . G . . END=9781 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 9782 . T . . END=9782 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,948 -20_10037292_10066351 9783 . T . . END=9783 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9784 . C . . END=9784 GT:DP:GQ:MIN_DP:PL 0/0:31:66:31:0,66,973 -20_10037292_10066351 9785 . T . . END=9787 GT:DP:GQ:MIN_DP:PL 0/0:31:86:30:0,86,975 -20_10037292_10066351 9788 . A . . END=9789 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9790 . A . . END=9792 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,955 -20_10037292_10066351 9793 . A . . END=9793 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9794 . T . . END=9794 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 9795 . A . . END=9796 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1015 -20_10037292_10066351 9797 . G . . END=9797 GT:DP:GQ:MIN_DP:PL 0/0:35:64:35:0,64,953 -20_10037292_10066351 9798 . A . . END=9801 GT:DP:GQ:MIN_DP:PL 0/0:36:91:35:0,91,1068 -20_10037292_10066351 9802 . T . . END=9809 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 9810 . A . . END=9810 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1101 -20_10037292_10066351 9811 . A . . END=9818 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 9819 . T . . END=9820 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1112 -20_10037292_10066351 9821 . T . . END=9830 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 9831 . A . . END=9831 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1115 -20_10037292_10066351 9832 . G . . END=9848 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1122 -20_10037292_10066351 9849 . A . . END=9849 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1030 -20_10037292_10066351 9850 . C . . END=9851 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1173 -20_10037292_10066351 9852 . C . . END=9852 GT:DP:GQ:MIN_DP:PL 0/0:37:52:37:0,52,971 -20_10037292_10066351 9853 . C . . END=9855 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1135 -20_10037292_10066351 9856 . C . . END=9856 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1125 -20_10037292_10066351 9857 . C . . END=9859 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1530 -20_10037292_10066351 12912 . G . . END=12912 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1203 -20_10037292_10066351 12913 . A . . END=12913 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 12914 . G . . END=12914 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1239 -20_10037292_10066351 12915 . C . . END=12935 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1157 -20_10037292_10066351 12936 . T . . END=12936 GT:DP:GQ:MIN_DP:PL 0/0:41:76:41:0,76,1212 -20_10037292_10066351 12937 . T . . END=12942 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,105,1575 -20_10037292_10066351 12943 . A . . END=12943 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1236 -20_10037292_10066351 12944 . A . . END=12978 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,105,1107 -20_10037292_10066351 12979 . A . . END=12979 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1213 -20_10037292_10066351 12980 . G . . END=12983 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1193 -20_10037292_10066351 12984 . G . . END=12984 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1260 -20_10037292_10066351 12985 . A . . END=13012 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,102,1146 -20_10037292_10066351 13013 . A . . END=13013 GT:DP:GQ:MIN_DP:PL 0/0:41:92:41:0,92,1181 -20_10037292_10066351 13014 . A . . END=13016 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1138 -20_10037292_10066351 13017 . C . . END=13017 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1020 -20_10037292_10066351 13018 . G . . END=13023 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,105,1575 -20_10037292_10066351 13024 . A . . END=13024 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,1028 -20_10037292_10066351 13025 . A . . END=13028 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,101,1192 -20_10037292_10066351 13029 . T . . END=13029 GT:DP:GQ:MIN_DP:PL 0/0:42:86:42:0,86,1160 -20_10037292_10066351 13030 . A . . END=13032 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,108,1620 -20_10037292_10066351 13033 . G . . END=13033 GT:DP:GQ:MIN_DP:PL 0/0:42:81:42:0,81,1210 -20_10037292_10066351 13034 . A . . END=13034 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1575 -20_10037292_10066351 13035 . G . . END=13035 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1181 -20_10037292_10066351 13036 . T . . END=13054 GT:DP:GQ:MIN_DP:PL 0/0:40:99:36:0,99,1182 -20_10037292_10066351 13055 . T . . END=13055 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1060 -20_10037292_10066351 13056 . C . . END=13057 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1145 -20_10037292_10066351 13058 . A . . END=13058 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1067 -20_10037292_10066351 13059 . T . . END=13060 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1124 -20_10037292_10066351 13061 . G . . END=13061 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1045 -20_10037292_10066351 13062 . G . . END=13062 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,107,1074 -20_10037292_10066351 13063 . T . . END=13063 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1106 -20_10037292_10066351 13064 . T . . END=13070 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,108,1620 -20_10037292_10066351 13071 . T . . END=13071 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1199 -20_10037292_10066351 13072 . T . . END=13078 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,104,1206 -20_10037292_10066351 13079 . A . . END=13079 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1440 -20_10037292_10066351 13080 . G . . END=13082 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,99,1485 -20_10037292_10066351 13083 . T . . END=13083 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1186 -20_10037292_10066351 13084 . C . . END=13090 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1207 -20_10037292_10066351 13091 . G . . END=13091 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1168 -20_10037292_10066351 13092 . T . . END=13092 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1137 -20_10037292_10066351 13093 . G . . END=13175 GT:DP:GQ:MIN_DP:PL 0/0:47:99:38:0,106,1209 -20_10037292_10066351 13176 . C . . END=13176 GT:DP:GQ:MIN_DP:PL 0/0:45:76:45:0,76,1292 -20_10037292_10066351 13177 . T . . END=13203 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,101,1297 -20_10037292_10066351 13204 . G . . END=13204 GT:DP:GQ:MIN_DP:PL 0/0:46:89:46:0,89,1350 -20_10037292_10066351 13205 . T . . END=13220 GT:DP:GQ:MIN_DP:PL 0/0:46:99:41:0,109,1372 -20_10037292_10066351 13221 . T . . END=13221 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1139 -20_10037292_10066351 13222 . A . . END=13261 GT:DP:GQ:MIN_DP:PL 0/0:40:99:33:0,99,1021 -20_10037292_10066351 13262 . A . . END=13262 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1069 -20_10037292_10066351 13263 . A . . END=13266 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 13267 . G . . END=13269 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1215 -20_10037292_10066351 13270 . A . . END=13283 GT:DP:GQ:MIN_DP:PL 0/0:34:72:27:0,72,1080 -20_10037292_10066351 13284 . G . . END=13284 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,767 -20_10037292_10066351 13285 . C . . END=13287 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 13288 . G . . END=13288 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13289 . T . . END=13289 GT:DP:GQ:MIN_DP:PL 0/0:29:65:29:0,65,809 -20_10037292_10066351 13290 . C . . END=13294 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,828 -20_10037292_10066351 13295 . T . . END=13306 GT:DP:GQ:MIN_DP:PL 0/0:27:78:26:0,78,767 -20_10037292_10066351 13307 . T . . END=13309 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,798 -20_10037292_10066351 13310 . T . . END=13312 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,890 -20_10037292_10066351 13313 . T . . END=13314 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1026 -20_10037292_10066351 13315 . T . . END=13321 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1018 -20_10037292_10066351 13322 . C . . END=13329 GT:DP:GQ:MIN_DP:PL 0/0:33:81:30:0,81,1215 -20_10037292_10066351 13330 . C . . END=13330 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,958 -20_10037292_10066351 13331 . A . . END=13344 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 13345 . C . . END=13345 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13346 . T . . END=13348 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13349 . G . . END=13349 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13350 . A . . END=13352 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13353 . T . . END=13355 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13356 . C . . END=13356 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13357 . T . . END=13360 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13361 . A . . END=13371 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 13372 . A . . END=13372 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,873 -20_10037292_10066351 13373 . A . . END=13377 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13378 . T . . END=13378 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20_10037292_10066351 13379 . G . . END=13383 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 13384 . G . . END=13384 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,939 -20_10037292_10066351 13385 . T . . END=13392 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,987 -20_10037292_10066351 13393 . C . . END=13393 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13394 . A . . END=13395 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13396 . C . . END=13399 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 13400 . T . . END=13404 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13405 . T . . END=13405 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1033 -20_10037292_10066351 13406 . C . . END=13418 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1017 -20_10037292_10066351 13419 . G . . END=13419 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1024 -20_10037292_10066351 13420 . C . . END=13428 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13429 . T . . END=13430 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1097 -20_10037292_10066351 13431 . G . . END=13433 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13434 . A . . END=13434 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1012 -20_10037292_10066351 13435 . A . . END=13438 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13439 . G . . END=13439 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,934 -20_10037292_10066351 13440 . T . . END=13440 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 13441 . T . . END=13441 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,996 -20_10037292_10066351 13442 . T . . END=13444 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 13445 . C . . END=13449 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,966 -20_10037292_10066351 13450 . C . . END=13451 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13452 . G . . END=13460 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1012 -20_10037292_10066351 13461 . T . . END=13461 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,987 -20_10037292_10066351 13462 . T . . END=13462 GT:DP:GQ:MIN_DP:PL 0/0:35:54:35:0,54,861 -20_10037292_10066351 13463 . C . . END=13463 GT:DP:GQ:MIN_DP:PL 0/0:33:32:33:0,32,865 -20_10037292_10066351 13464 . T . . END=13535 GT:DP:GQ:MIN_DP:PL 0/0:44:99:36:0,99,1095 -20_10037292_10066351 13536 . T C, 437.64 . BaseQRankSum=1.454;DP=45;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=162000,45;ReadPosRankSum=-1.613 GT:AD:DP:GQ:PL:SB 0/1:26,18,0:44:99:445,0,672,523,726,1249:15,11,11,7 -20_10037292_10066351 13537 . T . . END=13548 GT:DP:GQ:MIN_DP:PL 0/0:45:99:40:0,111,1665 -20_10037292_10066351 13549 . A . . END=13549 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1215 -20_10037292_10066351 13550 . G . . END=13554 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,100,1128 -20_10037292_10066351 13555 . A . . END=13556 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1079 -20_10037292_10066351 13557 . A . . END=13561 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 13562 . C . . END=13562 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1093 -20_10037292_10066351 13563 . T . . END=13563 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 13564 . G . . END=13564 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1104 -20_10037292_10066351 13565 . C . . END=13565 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 13566 . C . . END=13566 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1134 -20_10037292_10066351 13567 . C . . END=13577 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1146 -20_10037292_10066351 13578 . T . . END=13578 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1063 -20_10037292_10066351 13579 . A . . END=13579 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13580 . G . . END=13588 GT:DP:GQ:MIN_DP:PL 0/0:36:96:33:0,96,1440 -20_10037292_10066351 13589 . T . . END=13589 GT:DP:GQ:MIN_DP:PL 0/0:33:79:33:0,79,939 -20_10037292_10066351 13590 . G . . END=13590 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,991 -20_10037292_10066351 13591 . T . . END=13591 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,960 -20_10037292_10066351 13592 . C . . END=13592 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,966 -20_10037292_10066351 13593 . A . . END=13593 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 13594 . G . . END=13595 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,958 -20_10037292_10066351 13596 . T . . END=13596 GT:DP:GQ:MIN_DP:PL 0/0:35:75:35:0,75,994 -20_10037292_10066351 13597 . G . . END=13599 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13600 . T . . END=13603 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13604 . T . . END=13604 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1031 -20_10037292_10066351 13605 . C . . END=13605 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13606 . T . . END=13607 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 13608 . A . . END=13610 GT:DP:GQ:MIN_DP:PL 0/0:36:83:35:0,83,982 -20_10037292_10066351 13611 . A . . END=13617 GT:DP:GQ:MIN_DP:PL 0/0:36:90:33:0,90,1350 -20_10037292_10066351 13618 . T . . END=13631 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 13632 . A . . END=13632 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,941 -20_10037292_10066351 13633 . G . . END=13639 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13640 . C . . END=13640 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 13641 . A . . END=13654 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13655 . G . . END=13655 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,944 -20_10037292_10066351 13656 . C . . END=13657 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,980 -20_10037292_10066351 13658 . T . . END=13671 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,890 -20_10037292_10066351 13672 . T . . END=13684 GT:DP:GQ:MIN_DP:PL 0/0:34:83:32:0,83,982 -20_10037292_10066351 13685 . G . . END=13686 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13687 . A . . END=13687 GT:DP:GQ:MIN_DP:PL 0/0:30:69:30:0,69,896 -20_10037292_10066351 13688 . A . . END=13703 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,879 -20_10037292_10066351 13704 . C . . END=13704 GT:DP:GQ:MIN_DP:PL 0/0:33:52:33:0,52,943 -20_10037292_10066351 13705 . C . . END=13707 GT:DP:GQ:MIN_DP:PL 0/0:33:93:31:0,93,874 -20_10037292_10066351 13708 . C . . END=13708 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 13709 . C . . END=13709 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,983 -20_10037292_10066351 13710 . G . . END=13715 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 13716 . T . . END=13716 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1076 -20_10037292_10066351 13717 . C . . END=13717 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 13718 . A . . END=13718 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1070 -20_10037292_10066351 13719 . G . . END=13726 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,102,1091 -20_10037292_10066351 13727 . A . . END=13727 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1125 -20_10037292_10066351 13728 . A . . END=13757 GT:DP:GQ:MIN_DP:PL 0/0:40:99:36:0,99,1146 -20_10037292_10066351 13758 . A . . END=13758 GT:DP:GQ:MIN_DP:PL 0/0:36:61:36:0,61,1017 -20_10037292_10066351 13759 . T . . END=13767 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1019 -20_10037292_10066351 13768 . T . . END=13768 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 13769 . G . . END=13771 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 13772 . T . . END=13776 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 13777 . A . . END=13778 GT:DP:GQ:MIN_DP:PL 0/0:35:87:34:0,87,1305 -20_10037292_10066351 13779 . C . . END=13779 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,969 -20_10037292_10066351 13780 . A . . END=13797 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 13798 . T . . END=13802 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20_10037292_10066351 13803 . C . . END=13804 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 13805 . G . . END=13805 GT:DP:GQ:MIN_DP:PL 0/0:30:71:30:0,71,951 -20_10037292_10066351 13806 . C . . END=13807 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 13808 . T . . END=13815 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 13816 . A . . END=13840 GT:DP:GQ:MIN_DP:PL 0/0:30:80:27:0,80,850 -20_10037292_10066351 13841 . A . . END=13843 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13844 . A . . END=13847 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13848 . G . . END=13848 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13849 . T . . END=13859 GT:DP:GQ:MIN_DP:PL 0/0:31:74:28:0,74,918 -20_10037292_10066351 13860 . T . . END=13862 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,835 -20_10037292_10066351 13863 . T . . END=13873 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 13874 . T . . END=13880 GT:DP:GQ:MIN_DP:PL 0/0:28:69:27:0,69,845 -20_10037292_10066351 13881 . A . . END=13881 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 13882 . C . . END=13882 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,1035 -20_10037292_10066351 13883 . C . . END=13883 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,750 -20_10037292_10066351 13884 . T . . END=13899 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,722 -20_10037292_10066351 13900 . A . . END=13900 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,739 -20_10037292_10066351 13901 . T . . END=13901 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,766 -20_10037292_10066351 13902 . A . . END=13902 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 13903 . A . . END=13903 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,701 -20_10037292_10066351 13904 . A . . END=13905 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 13906 . A . . END=13921 GT:DP:GQ:MIN_DP:PL 0/0:26:72:24:0,72,735 -20_10037292_10066351 13922 . G . . END=13922 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,737 -20_10037292_10066351 13923 . C . . END=13932 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,806 -20_10037292_10066351 13933 . T . . END=13933 GT:DP:GQ:MIN_DP:PL 0/0:26:52:26:0,52,811 -20_10037292_10066351 13934 . G . . END=13942 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 13943 . A . . END=13943 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13944 . C . . END=13946 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 13947 . G . . END=13948 GT:DP:GQ:MIN_DP:PL 0/0:28:67:28:0,67,785 -20_10037292_10066351 13949 . A . . END=13952 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 13953 . T . . END=13954 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 13955 . G . . END=13957 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 13958 . A . . END=13958 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,843 -20_10037292_10066351 13959 . C . . END=13961 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 13962 . C . . END=13962 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,774 -20_10037292_10066351 13963 . T . . END=13963 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 13964 . G . . END=13973 GT:DP:GQ:MIN_DP:PL 0/0:26:66:25:0,66,798 -20_10037292_10066351 13974 . A . . END=13974 GT:DP:GQ:MIN_DP:PL 0/0:25:59:25:0,59,721 -20_10037292_10066351 13975 . G . . END=13976 GT:DP:GQ:MIN_DP:PL 0/0:25:66:24:0,66,990 -20_10037292_10066351 13977 . C . . END=13977 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,723 -20_10037292_10066351 13978 . T . . END=13985 GT:DP:GQ:MIN_DP:PL 0/0:25:66:24:0,66,990 -20_10037292_10066351 13986 . G . . END=13988 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,1080 -20_10037292_10066351 13989 . T . . END=13991 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 -20_10037292_10066351 13992 . A . . END=13992 GT:DP:GQ:MIN_DP:PL 0/0:25:55:25:0,55,697 -20_10037292_10066351 13993 . A . . END=13993 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 13994 . T . . END=13994 GT:DP:GQ:MIN_DP:PL 0/0:25:62:25:0,62,748 -20_10037292_10066351 13995 . T . . END=14002 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,808 -20_10037292_10066351 14003 . A . . END=14003 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,742 -20_10037292_10066351 14004 . A . . END=14006 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 14007 . C . . END=14013 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 -20_10037292_10066351 14014 . G . . END=14020 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 14021 . G . . END=14024 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 14025 . C . . END=14034 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 14035 . A . . END=14041 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 14042 . G . . END=14044 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 14045 . G . . END=14046 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 14047 . A . . END=14049 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 14050 . G . . END=14051 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,933 -20_10037292_10066351 14052 . G . . END=14055 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 14056 . G . . END=14056 GT:DP:GQ:MIN_DP:PL 0/0:32:85:32:0,85,933 -20_10037292_10066351 14057 . T . . END=14061 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,938 -20_10037292_10066351 14062 . A . . END=14062 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,925 -20_10037292_10066351 14063 . G . . END=14064 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,876 -20_10037292_10066351 14065 . T . . END=14065 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,778 -20_10037292_10066351 14066 . G . . END=14070 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 14071 . A . . END=14084 GT:DP:GQ:MIN_DP:PL 0/0:28:72:26:0,72,1080 -20_10037292_10066351 14085 . C . . END=14085 GT:DP:GQ:MIN_DP:PL 0/0:27:51:27:0,51,814 -20_10037292_10066351 14086 . C . . END=14086 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,791 -20_10037292_10066351 14087 . A . . END=14087 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 14088 . G . . END=14088 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,809 -20_10037292_10066351 14089 . C . . END=14095 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,796 -20_10037292_10066351 14096 . G . . END=14101 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 14102 . T . . END=14102 GT:DP:GQ:MIN_DP:PL 0/0:28:55:28:0,55,788 -20_10037292_10066351 14103 . C . . END=14112 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,879 -20_10037292_10066351 14113 . A . . END=14122 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,1080 -20_10037292_10066351 14123 . G . . END=14123 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,865 -20_10037292_10066351 14124 . C . . END=14129 GT:DP:GQ:MIN_DP:PL 0/0:27:72:24:0,72,686 -20_10037292_10066351 14130 . A . . END=14139 GT:DP:GQ:MIN_DP:PL 0/0:25:60:23:0,60,900 -20_10037292_10066351 14140 . A . . END=14141 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 -20_10037292_10066351 14142 . C . . END=14144 GT:DP:GQ:MIN_DP:PL 0/0:22:54:21:0,54,810 -20_10037292_10066351 14145 . T . . END=14146 GT:DP:GQ:MIN_DP:PL 0/0:21:51:21:0,51,765 -20_10037292_10066351 14147 . A . . END=14150 GT:DP:GQ:MIN_DP:PL 0/0:22:54:21:0,54,810 -20_10037292_10066351 14151 . T . . END=14154 GT:DP:GQ:MIN_DP:PL 0/0:20:51:19:0,51,765 -20_10037292_10066351 14155 . T . . END=14155 GT:DP:GQ:MIN_DP:PL 0/0:21:50:21:0,50,612 -20_10037292_10066351 14156 . T C, 183.64 . BaseQRankSum=0.703;DP=20;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=72000,20;ReadPosRankSum=-0.193 GT:AD:DP:GQ:PL:SB 0/1:12,8,0:20:99:191,0,319,227,343,570:5,7,5,3 -20_10037292_10066351 14157 . T . . END=14158 GT:DP:GQ:MIN_DP:PL 0/0:21:51:20:0,51,765 -20_10037292_10066351 14159 . T . . END=14159 GT:DP:GQ:MIN_DP:PL 0/0:20:48:20:0,48,720 -20_10037292_10066351 14160 . C . . END=14160 GT:DP:GQ:MIN_DP:PL 0/0:20:46:20:0,46,579 -20_10037292_10066351 14161 . C . . END=14161 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 -20_10037292_10066351 14162 . C . . END=14162 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 -20_10037292_10066351 14163 . C . . END=14164 GT:DP:GQ:MIN_DP:PL 0/0:22:57:22:0,57,855 -20_10037292_10066351 14165 . T . . END=14169 GT:DP:GQ:MIN_DP:PL 0/0:22:60:21:0,60,900 -20_10037292_10066351 14170 . C . . END=14170 GT:DP:GQ:MIN_DP:PL 0/0:22:48:22:0,48,666 -20_10037292_10066351 14171 . A . . END=14172 GT:DP:GQ:MIN_DP:PL 0/0:22:63:22:0,63,945 -20_10037292_10066351 14173 . T . . END=14173 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,714 -20_10037292_10066351 14174 . C . . END=14174 GT:DP:GQ:MIN_DP:PL 0/0:25:61:25:0,61,767 -20_10037292_10066351 14175 . A . . END=14176 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,785 -20_10037292_10066351 14177 . C . . END=14178 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,792 -20_10037292_10066351 14179 . C . . END=14187 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,778 -20_10037292_10066351 14188 . C . . END=14188 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 14189 . C . . END=14192 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 14193 . T . . END=14197 GT:DP:GQ:MIN_DP:PL 0/0:25:60:25:0,60,715 -20_10037292_10066351 14198 . A . . END=14209 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,750 -20_10037292_10066351 14210 . A . . END=14211 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,824 -20_10037292_10066351 14212 . G . . END=14212 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,802 -20_10037292_10066351 14213 . G . . END=14214 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 14215 . G . . END=14217 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,933 -20_10037292_10066351 14218 . T . . END=14218 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,874 -20_10037292_10066351 14219 . T . . END=14219 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,972 -20_10037292_10066351 14220 . G . . END=14220 GT:DP:GQ:MIN_DP:PL 0/0:31:75:31:0,75,937 -20_10037292_10066351 14221 . G . . END=14222 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,936 -20_10037292_10066351 14223 . T . . END=14224 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1004 -20_10037292_10066351 14225 . G . . END=14228 GT:DP:GQ:MIN_DP:PL 0/0:33:93:31:0,93,930 -20_10037292_10066351 14229 . C . . END=14230 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 14231 . T . . END=14232 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14233 . C . . END=14233 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1043 -20_10037292_10066351 14234 . A . . END=14235 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 14236 . G . . END=14236 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1041 -20_10037292_10066351 14237 . A . . END=14237 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 14238 . T . . END=14238 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1030 -20_10037292_10066351 14239 . T . . END=14239 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14240 . T . . END=14247 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1077 -20_10037292_10066351 14248 . G . . END=14248 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1046 -20_10037292_10066351 14249 . A . . END=14249 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,949 -20_10037292_10066351 14250 . T . . END=14250 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1084 -20_10037292_10066351 14251 . T . . END=14251 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1020 -20_10037292_10066351 14252 . T . . END=14406 GT:DP:GQ:MIN_DP:PL 0/0:48:99:37:0,109,1169 -20_10037292_10066351 14407 . C . . END=14407 GT:DP:GQ:MIN_DP:PL 0/0:52:84:52:0,84,1360 -20_10037292_10066351 14408 . T . . END=14510 GT:DP:GQ:MIN_DP:PL 0/0:53:99:46:0,118,1386 -20_10037292_10066351 14511 . G . . END=14511 GT:DP:GQ:MIN_DP:PL 0/0:47:95:47:0,95,1387 -20_10037292_10066351 14512 . T . . END=14557 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,102,1196 -20_10037292_10066351 14558 . C . . END=14558 GT:DP:GQ:MIN_DP:PL 0/0:36:77:36:0,77,1030 -20_10037292_10066351 14559 . C . . END=14563 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1157 -20_10037292_10066351 14564 . A . . END=14565 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 14566 . T . . END=14566 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 14567 . G . . END=14571 GT:DP:GQ:MIN_DP:PL 0/0:38:93:37:0,93,1145 -20_10037292_10066351 14572 . T . . END=14573 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 14574 . A . . END=14576 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 14577 . G . . END=14577 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1065 -20_10037292_10066351 14578 . T . . END=14578 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 14579 . G . . END=14579 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1029 -20_10037292_10066351 14580 . C . . END=14581 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 14582 . C . . END=14583 GT:DP:GQ:MIN_DP:PL 0/0:33:73:33:0,73,985 -20_10037292_10066351 14584 . C . . END=14586 GT:DP:GQ:MIN_DP:PL 0/0:35:81:34:0,81,1215 -20_10037292_10066351 14587 . A . . END=14589 GT:DP:GQ:MIN_DP:PL 0/0:35:78:34:0,78,1170 -20_10037292_10066351 14590 . T . . END=14590 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1035 -20_10037292_10066351 14591 . A . . END=14597 GT:DP:GQ:MIN_DP:PL 0/0:35:72:27:0,72,1024 -20_10037292_10066351 14598 . T . . END=14598 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,836 -20_10037292_10066351 14599 . A . . END=14601 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,854 -20_10037292_10066351 14602 . G . . END=14603 GT:DP:GQ:MIN_DP:PL 0/0:27:63:26:0,63,794 -20_10037292_10066351 14604 . C . . END=14612 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 -20_10037292_10066351 14613 . T . . END=14613 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,803 -20_10037292_10066351 14614 . A . . END=14617 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,822 -20_10037292_10066351 14618 . A . . END=14619 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 14620 . T . . END=14620 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,845 -20_10037292_10066351 14621 . C . . END=14626 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 14627 . T . . END=14627 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,946 -20_10037292_10066351 14628 . T . . END=14629 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,980 -20_10037292_10066351 14630 . A . . END=14634 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 14635 . A . . END=14636 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 14637 . A . . END=14649 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 14650 . T . . END=14653 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 14654 . A . . END=14656 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 14657 . T . . END=14657 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1040 -20_10037292_10066351 14658 . C . . END=14671 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 14672 . T . . END=14672 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,910 -20_10037292_10066351 14673 . T . . END=14673 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,1002 -20_10037292_10066351 14674 . G . . END=14674 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,839 -20_10037292_10066351 14675 . A . . END=14680 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,950 -20_10037292_10066351 14681 . A . . END=14681 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1051 -20_10037292_10066351 14682 . T . . END=14682 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,979 -20_10037292_10066351 14683 . C . . END=14683 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 14684 . T . . END=14684 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1045 -20_10037292_10066351 14685 . T . . END=14685 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 14686 . A . . END=14686 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,1047 -20_10037292_10066351 14687 . A . . END=14689 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14690 . G . . END=14690 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,961 -20_10037292_10066351 14691 . T . . END=14691 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 14692 . T . . END=14692 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1090 -20_10037292_10066351 14693 . T . . END=14694 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 14695 . A . . END=14695 GT:DP:GQ:MIN_DP:PL 0/0:35:62:35:0,62,1010 -20_10037292_10066351 14696 . A . . END=14696 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1135 -20_10037292_10066351 14697 . A . . END=14698 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 14699 . T . . END=14699 GT:DP:GQ:MIN_DP:PL 0/0:38:55:38:0,55,1027 -20_10037292_10066351 14700 . A . . END=14703 GT:DP:GQ:MIN_DP:PL 0/0:37:91:37:0,91,1149 -20_10037292_10066351 14704 . A . . END=14704 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1106 -20_10037292_10066351 14705 . A . . END=14706 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1193 -20_10037292_10066351 14707 . A . . END=14707 GT:DP:GQ:MIN_DP:PL 0/0:37:64:37:0,64,1029 -20_10037292_10066351 14708 . A . . END=14709 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 14710 . T . . END=14712 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 14713 . T . . END=14713 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1128 -20_10037292_10066351 14714 . T . . END=14718 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1192 -20_10037292_10066351 14719 . T . . END=14719 GT:DP:GQ:MIN_DP:PL 0/0:36:82:36:0,82,1087 -20_10037292_10066351 14720 . T . . END=14737 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,100,1160 diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf.idx b/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf.idx deleted file mode 100644 index 63861603f..000000000 Binary files a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf.idx and /dev/null differ diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf b/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf deleted file mode 100644 index 63eccf733..000000000 --- a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf +++ /dev/null @@ -1,1672 +0,0 @@ -##fileformat=VCFv4.2 -##ALT= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) -##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) -##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) -##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) -##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) -##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) -##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) -##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) -##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) -##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) -##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) -##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) -##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) -##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) -##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) -##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) -##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) -##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) -##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) -##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) -##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) -##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) -##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) -##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) -##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) -##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) -##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) -##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) -##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) -##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) -##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) -##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) -##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) -##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) -##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) -##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) -##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) -##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) -##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) -##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) -##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) -##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) -##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) -##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) -##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) -##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) -##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) -##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) -##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) -##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) -##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) -##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) -##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) -##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) -##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) -##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) -##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) -##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) -##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) -##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) -##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) -##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) -##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) -##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) -##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive) -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_son -20_10037292_10066351 3277 . G . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,719 -20_10037292_10066351 3283 . T . . END=3283 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,833 -20_10037292_10066351 3284 . T . . END=3287 GT:DP:GQ:MIN_DP:PL 0/0:29:78:27:0,78,1170 -20_10037292_10066351 3288 . A . . END=3290 GT:DP:GQ:MIN_DP:PL 0/0:32:84:31:0,84,1260 -20_10037292_10066351 3291 . G . . END=3291 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,1023 -20_10037292_10066351 3292 . G . . END=3293 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3294 . A . . END=3294 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,974 -20_10037292_10066351 3295 . A . . END=3297 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,986 -20_10037292_10066351 3298 . T . . END=3309 GT:DP:GQ:MIN_DP:PL 0/0:32:84:28:0,84,870 -20_10037292_10066351 3310 . A . . END=3310 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3311 . A . . END=3313 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 3314 . A . . END=3314 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,873 -20_10037292_10066351 3315 . C . . END=3315 GT:DP:GQ:MIN_DP:PL 0/0:30:69:30:0,69,894 -20_10037292_10066351 3316 . T . . END=3316 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 3317 . G . . END=3317 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,864 -20_10037292_10066351 3318 . T . . END=3318 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3319 . C . . END=3319 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,945 -20_10037292_10066351 3320 . A . . END=3333 GT:DP:GQ:MIN_DP:PL 0/0:32:84:30:0,84,993 -20_10037292_10066351 3334 . A . . END=3334 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,979 -20_10037292_10066351 3335 . G . . END=3338 GT:DP:GQ:MIN_DP:PL 0/0:30:86:29:0,86,836 -20_10037292_10066351 3339 . C . . END=3341 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3342 . C . . END=3342 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,870 -20_10037292_10066351 3343 . A . . END=3348 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,962 -20_10037292_10066351 3349 . A . . END=3349 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,1011 -20_10037292_10066351 3350 . G . . END=3351 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3352 . A . . END=3352 GT:DP:GQ:MIN_DP:PL 0/0:36:87:36:0,87,1121 -20_10037292_10066351 3353 . G . . END=3361 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1163 -20_10037292_10066351 3362 . C . . END=3362 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1036 -20_10037292_10066351 3363 . A . . END=3364 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 3365 . A . . END=3365 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1067 -20_10037292_10066351 3366 . C . . END=3369 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1142 -20_10037292_10066351 3370 . C . . END=3370 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1138 -20_10037292_10066351 3371 . A . . END=3418 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,108,1248 -20_10037292_10066351 3419 . T . . END=3419 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1188 -20_10037292_10066351 3420 . T . . END=3436 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1140 -20_10037292_10066351 3437 . T . . END=3437 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1118 -20_10037292_10066351 3438 . T . . END=3439 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,103,1164 -20_10037292_10066351 3440 . A . . END=3440 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1216 -20_10037292_10066351 3441 . T . . END=3444 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,105,1575 -20_10037292_10066351 3445 . G . . END=3446 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1100 -20_10037292_10066351 3447 . C . . END=3453 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 3454 . G . . END=3458 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1043 -20_10037292_10066351 3459 . T . . END=3459 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1134 -20_10037292_10066351 3460 . T . . END=3460 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 3461 . C . . END=3468 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,101,1112 -20_10037292_10066351 3469 . C . . END=3469 GT:DP:GQ:MIN_DP:PL 0/0:39:60:39:0,60,1079 -20_10037292_10066351 3470 . T . . END=3474 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,99,1485 -20_10037292_10066351 3475 . C . . END=3475 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1064 -20_10037292_10066351 3476 . T . . END=3478 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,102,1530 -20_10037292_10066351 3479 . T . . END=3479 GT:DP:GQ:MIN_DP:PL 0/0:44:57:44:0,57,1177 -20_10037292_10066351 3480 . C CT, 742.03 . DP=30;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=108000,30 GT:AD:DP:GQ:PL:SB 1/1:0,26,0:26:78:756,78,0,756,78,756:0,0,15,11 -20_10037292_10066351 3481 . T . . END=3486 GT:DP:GQ:MIN_DP:PL 0/0:28:72:26:0,72,1080 -20_10037292_10066351 3487 . T . . END=3487 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 3488 . T . . END=3489 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 3490 . C . . END=3490 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,818 -20_10037292_10066351 3491 . A . . END=3491 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3492 . A . . END=3492 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 3493 . T . . END=3496 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3497 . C . . END=3497 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,802 -20_10037292_10066351 3498 . A . . END=3498 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3499 . C . . END=3499 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 3500 . G . . END=3501 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 3502 . A . . END=3512 GT:DP:GQ:MIN_DP:PL 0/0:28:72:26:0,72,1080 -20_10037292_10066351 3513 . A . . END=3513 GT:DP:GQ:MIN_DP:PL 0/0:26:62:26:0,62,772 -20_10037292_10066351 3514 . T . . END=3519 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 3520 . AT A, 760.03 . DP=28;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=100800,28 GT:AD:DP:GQ:PL:SB 1/1:0,26,0:26:78:774,78,0,774,78,774:0,0,15,11 -20_10037292_10066351 3522 . T . . END=3523 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 3524 . T . . END=3524 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1092 -20_10037292_10066351 3525 . T . . END=3529 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1194 -20_10037292_10066351 3530 . A . . END=3531 GT:DP:GQ:MIN_DP:PL 0/0:39:92:38:0,92,1099 -20_10037292_10066351 3532 . A . . END=3532 GT:DP:GQ:MIN_DP:PL 0/0:38:65:38:0,65,1022 -20_10037292_10066351 3533 . A . . END=3535 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 3536 . G . . END=3536 GT:DP:GQ:MIN_DP:PL 0/0:39:67:39:0,67,996 -20_10037292_10066351 3537 . A . . END=3547 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1620 -20_10037292_10066351 3548 . G . . END=3548 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1042 -20_10037292_10066351 3549 . T . . END=3550 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1165 -20_10037292_10066351 3551 . A . . END=3551 GT:DP:GQ:MIN_DP:PL 0/0:38:94:38:0,94,1105 -20_10037292_10066351 3552 . A . . END=3552 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3553 . C . . END=3555 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1070 -20_10037292_10066351 3556 . C . . END=3562 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,100,1084 -20_10037292_10066351 3563 . C . . END=3563 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1080 -20_10037292_10066351 3564 . A . . END=3570 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,108,1206 -20_10037292_10066351 3571 . C . . END=3571 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1114 -20_10037292_10066351 3572 . A . . END=3576 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,102,1145 -20_10037292_10066351 3577 . G . . END=3577 GT:DP:GQ:MIN_DP:PL 0/0:41:83:41:0,83,1163 -20_10037292_10066351 3578 . A . . END=3579 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,112,1139 -20_10037292_10066351 3580 . T . . END=3580 GT:DP:GQ:MIN_DP:PL 0/0:43:94:43:0,94,1150 -20_10037292_10066351 3581 . T . . END=3593 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,100,1153 -20_10037292_10066351 3594 . C . . END=3595 GT:DP:GQ:MIN_DP:PL 0/0:40:94:39:0,94,1054 -20_10037292_10066351 3596 . T . . END=3596 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,109,1244 -20_10037292_10066351 3597 . C . . END=3597 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1101 -20_10037292_10066351 3598 . T . . END=3599 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,102,1530 -20_10037292_10066351 3600 . T . . END=3600 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1208 -20_10037292_10066351 3601 . T . . END=3601 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,105,1575 -20_10037292_10066351 3602 . A . . END=3603 GT:DP:GQ:MIN_DP:PL 0/0:41:75:40:0,75,1125 -20_10037292_10066351 3604 . G . . END=3604 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,105,1575 -20_10037292_10066351 3605 . C . . END=3605 GT:DP:GQ:MIN_DP:PL 0/0:42:62:42:0,62,1050 -20_10037292_10066351 3606 . C . . END=3611 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,99,1485 -20_10037292_10066351 3612 . G . . END=3612 GT:DP:GQ:MIN_DP:PL 0/0:39:63:39:0,63,1081 -20_10037292_10066351 3613 . T . . END=3613 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,102,1530 -20_10037292_10066351 3614 . G . . END=3614 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1152 -20_10037292_10066351 3615 . C . . END=3615 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,105,1575 -20_10037292_10066351 3616 . A . . END=3616 GT:DP:GQ:MIN_DP:PL 0/0:40:69:40:0,69,1125 -20_10037292_10066351 3617 . T . . END=3622 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1485 -20_10037292_10066351 3623 . T . . END=3623 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1048 -20_10037292_10066351 3624 . A . . END=3625 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1152 -20_10037292_10066351 3626 . G . . END=3628 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,105,1121 -20_10037292_10066351 3629 . T . . END=3629 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1081 -20_10037292_10066351 3630 . C . . END=3630 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1015 -20_10037292_10066351 3631 . T . . END=3631 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 3632 . C . . END=3632 GT:DP:GQ:MIN_DP:PL 0/0:34:59:34:0,59,951 -20_10037292_10066351 3633 . T . . END=3633 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1033 -20_10037292_10066351 3634 . C . . END=3634 GT:DP:GQ:MIN_DP:PL 0/0:35:68:35:0,68,974 -20_10037292_10066351 3635 . A . . END=3641 GT:DP:GQ:MIN_DP:PL 0/0:36:91:35:0,91,1085 -20_10037292_10066351 3642 . C . . END=3642 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,900 -20_10037292_10066351 3643 . G . . END=3651 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1171 -20_10037292_10066351 3652 . A . . END=3652 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1126 -20_10037292_10066351 3653 . G . . END=3667 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,99,1092 -20_10037292_10066351 3668 . A . . END=3668 GT:DP:GQ:MIN_DP:PL 0/0:44:76:44:0,76,1248 -20_10037292_10066351 3669 . T . . END=3672 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,120,1800 -20_10037292_10066351 3673 . T . . END=3673 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1192 -20_10037292_10066351 3674 . G . . END=3674 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,101,1251 -20_10037292_10066351 3675 . A . . END=3675 GT:DP:GQ:MIN_DP:PL 0/0:42:88:42:0,88,1126 -20_10037292_10066351 3676 . A . . END=3683 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,113,1311 -20_10037292_10066351 3684 . C . . END=3684 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1257 -20_10037292_10066351 3685 . T . . END=3685 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,120,1800 -20_10037292_10066351 3686 . C . . END=3686 GT:DP:GQ:MIN_DP:PL 0/0:43:93:43:0,93,1225 -20_10037292_10066351 3687 . C . . END=3693 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,113,1254 -20_10037292_10066351 3694 . A . . END=3694 GT:DP:GQ:MIN_DP:PL 0/0:44:80:44:0,80,1185 -20_10037292_10066351 3695 . G . . END=3769 GT:DP:GQ:MIN_DP:PL 0/0:47:99:41:0,100,1196 -20_10037292_10066351 3770 . A . . END=3770 GT:DP:GQ:MIN_DP:PL 0/0:48:88:48:0,88,1268 -20_10037292_10066351 3771 . A . . END=3780 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,106,1300 -20_10037292_10066351 3781 . C . . END=3781 GT:DP:GQ:MIN_DP:PL 0/0:44:85:44:0,85,1222 -20_10037292_10066351 3782 . T . . END=3784 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,120,1800 -20_10037292_10066351 3785 . G . . END=3785 GT:DP:GQ:MIN_DP:PL 0/0:44:97:44:0,97,1329 -20_10037292_10066351 3786 . T . . END=3834 GT:DP:GQ:MIN_DP:PL 0/0:44:99:36:0,105,1125 -20_10037292_10066351 3835 . T . . END=3835 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1163 -20_10037292_10066351 3836 . C . . END=3836 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3837 . C . . END=3837 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1117 -20_10037292_10066351 3838 . T . . END=3857 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1041 -20_10037292_10066351 3858 . G . . END=3867 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 3868 . T . . END=3868 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,911 -20_10037292_10066351 3869 . G . . END=3870 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 3871 . A . . END=3871 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,927 -20_10037292_10066351 3872 . C . . END=3872 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 3873 . T . . END=3873 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,914 -20_10037292_10066351 3874 . G . . END=3877 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 3878 . A . . END=3883 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 3884 . T . . END=3884 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 3885 . T . . END=3885 GT:DP:GQ:MIN_DP:PL 0/0:35:79:35:0,79,1031 -20_10037292_10066351 3886 . C . . END=3890 GT:DP:GQ:MIN_DP:PL 0/0:35:81:34:0,81,1215 -20_10037292_10066351 3891 . G . . END=3893 GT:DP:GQ:MIN_DP:PL 0/0:38:90:35:0,90,1137 -20_10037292_10066351 3894 . C . . END=3899 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,1485 -20_10037292_10066351 3900 . C . . END=3900 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1069 -20_10037292_10066351 3901 . A . . END=3901 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 3902 . A . . END=3902 GT:DP:GQ:MIN_DP:PL 0/0:38:54:38:0,54,1082 -20_10037292_10066351 3903 . G . . END=3906 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 3907 . G . . END=3907 GT:DP:GQ:MIN_DP:PL 0/0:37:88:37:0,88,1135 -20_10037292_10066351 3908 . C . . END=3929 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1183 -20_10037292_10066351 3930 . T . . END=3936 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 3937 . A . . END=3942 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 3943 . T . . END=3948 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,960 -20_10037292_10066351 3949 . A . . END=3949 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,932 -20_10037292_10066351 3950 . G . . END=3955 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,959 -20_10037292_10066351 3956 . A . . END=3956 GT:DP:GQ:MIN_DP:PL 0/0:31:70:31:0,70,941 -20_10037292_10066351 3957 . C . . END=3965 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,920 -20_10037292_10066351 3966 . T . . END=3966 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1005 -20_10037292_10066351 3967 . A . . END=3967 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3968 . G . . END=3968 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,1014 -20_10037292_10066351 3969 . C . . END=3975 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 3976 . A . . END=3980 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 -20_10037292_10066351 3981 . A . . END=3983 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,917 -20_10037292_10066351 3984 . A . . END=3987 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 3988 . G . . END=3997 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,914 -20_10037292_10066351 3998 . T . . END=4000 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4001 . A . . END=4001 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1030 -20_10037292_10066351 4002 . A . . END=4006 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1047 -20_10037292_10066351 4007 . C . . END=4007 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1026 -20_10037292_10066351 4008 . A . . END=4010 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4011 . T . . END=4011 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 4012 . C T, 1092.06 . DP=36;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=129600,36 GT:AD:DP:GQ:PL:SB 1/1:0,35,0:35:99:1106,105,0,1106,105,1106:0,0,19,16 -20_10037292_10066351 4013 . G . . END=4013 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 4014 . G . . END=4017 GT:DP:GQ:MIN_DP:PL 0/0:37:90:35:0,90,1350 -20_10037292_10066351 4018 . A . . END=4019 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,1170 -20_10037292_10066351 4020 . T . . END=4024 GT:DP:GQ:MIN_DP:PL 0/0:36:81:35:0,81,1215 -20_10037292_10066351 4025 . A . . END=4031 GT:DP:GQ:MIN_DP:PL 0/0:33:72:28:0,72,1080 -20_10037292_10066351 4032 . T . . END=4034 GT:DP:GQ:MIN_DP:PL 0/0:30:66:28:0,66,990 -20_10037292_10066351 4035 . G T, 0 . BaseQRankSum=-2.303;DP=30;ExcessHet=0.0000;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=108000,30;ReadPosRankSum=1.760 GT:AD:DP:GQ:PL:SB 0/0:25,2,0:27:60:0,60,734,74,739,753:14,11,1,1 -20_10037292_10066351 4036 . T . . END=4040 GT:DP:GQ:MIN_DP:PL 0/0:27:63:26:0,63,945 -20_10037292_10066351 4041 . T . . END=4043 GT:DP:GQ:MIN_DP:PL 0/0:29:75:27:0,75,1125 -20_10037292_10066351 4044 . T . . END=4050 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 4051 . C . . END=4053 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 4054 . G . . END=4061 GT:DP:GQ:MIN_DP:PL 0/0:31:81:28:0,81,1215 -20_10037292_10066351 4062 . A . . END=4066 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4067 . C . . END=4067 GT:DP:GQ:MIN_DP:PL 0/0:32:73:32:0,73,937 -20_10037292_10066351 4068 . A . . END=4081 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,101,1033 -20_10037292_10066351 4082 . C . . END=4082 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1154 -20_10037292_10066351 4083 . T . . END=4106 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1167 -20_10037292_10066351 4107 . G . . END=4107 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1286 -20_10037292_10066351 4108 . G . . END=4139 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1071 -20_10037292_10066351 4140 . T . . END=4141 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1135 -20_10037292_10066351 4142 . A . . END=4177 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,100,1167 -20_10037292_10066351 4178 . A . . END=4186 GT:DP:GQ:MIN_DP:PL 0/0:38:90:36:0,90,1350 -20_10037292_10066351 4187 . T . . END=4191 GT:DP:GQ:MIN_DP:PL 0/0:37:87:33:0,87,1305 -20_10037292_10066351 4192 . G . . END=4192 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4193 . A . . END=4193 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,1028 -20_10037292_10066351 4194 . C . . END=4194 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4195 . T . . END=4196 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1066 -20_10037292_10066351 4197 . T . . END=4200 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1040 -20_10037292_10066351 4201 . G . . END=4201 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1117 -20_10037292_10066351 4202 . G . . END=4208 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4209 . G . . END=4210 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 4211 . C . . END=4212 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 4213 . T . . END=4214 GT:DP:GQ:MIN_DP:PL 0/0:38:93:37:0,93,1395 -20_10037292_10066351 4215 . A . . END=4219 GT:DP:GQ:MIN_DP:PL 0/0:37:80:34:0,80,1158 -20_10037292_10066351 4220 . T . . END=4225 GT:DP:GQ:MIN_DP:PL 0/0:36:93:34:0,93,1395 -20_10037292_10066351 4226 . G . . END=4226 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1017 -20_10037292_10066351 4227 . T . . END=4232 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 4233 . C . . END=4233 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1039 -20_10037292_10066351 4234 . C . . END=4235 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,101,1014 -20_10037292_10066351 4236 . A . . END=4236 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,1043 -20_10037292_10066351 4237 . T . . END=4376 GT:DP:GQ:MIN_DP:PL 0/0:46:99:36:0,105,1190 -20_10037292_10066351 4377 . T . . END=4377 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1282 -20_10037292_10066351 4378 . C . . END=4389 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,102,1234 -20_10037292_10066351 4390 . A . . END=4390 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1120 -20_10037292_10066351 4391 . T . . END=4391 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1119 -20_10037292_10066351 4392 . C . . END=4393 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4394 . A . . END=4398 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 4399 . A . . END=4399 GT:DP:GQ:MIN_DP:PL 0/0:36:88:36:0,88,1098 -20_10037292_10066351 4400 . T . . END=4403 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1070 -20_10037292_10066351 4404 . A . . END=4404 GT:DP:GQ:MIN_DP:PL 0/0:35:28:35:0,28,953 -20_10037292_10066351 4405 . A . . END=4405 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 4406 . C . . END=4407 GT:DP:GQ:MIN_DP:PL 0/0:28:66:28:0,66,990 -20_10037292_10066351 4408 . T . . END=4408 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 4409 . A ATG,ATATG, 785.03 . DP=31;ExcessHet=0.0000;MLEAC=0,2,0;MLEAF=0.00,1.00,0.00;RAW_MQandDP=111600,31 GT:AD:DP:GQ:PL:SB 2/2:0,0,24,0:24:72:799,867,1161,72,87,0,850,1031,87,980:0,0,13,11 -20_10037292_10066351 4410 . T . . END=4410 GT:DP:GQ:MIN_DP:PL 0/0:35:81:35:0,81,1215 -20_10037292_10066351 4411 . G . . END=4411 GT:DP:GQ:MIN_DP:PL 0/0:34:0:34:0,0,738 -20_10037292_10066351 4412 . T . . END=4412 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 4413 . G . . END=4416 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 -20_10037292_10066351 4417 . G . . END=4422 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 4423 . G . . END=4423 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1108 -20_10037292_10066351 4424 . T . . END=4426 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 4427 . G . . END=4427 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1091 -20_10037292_10066351 4428 . T . . END=4430 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1137 -20_10037292_10066351 4431 . G . . END=4435 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 4436 . C . . END=4436 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1161 -20_10037292_10066351 4437 . A . . END=4473 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,108,1286 -20_10037292_10066351 4474 . A . . END=4474 GT:DP:GQ:MIN_DP:PL 0/0:45:87:45:0,87,1273 -20_10037292_10066351 4475 . G . . END=4479 GT:DP:GQ:MIN_DP:PL 0/0:46:99:44:0,103,1305 -20_10037292_10066351 4480 . G . . END=4480 GT:DP:GQ:MIN_DP:PL 0/0:46:89:46:0,89,1235 -20_10037292_10066351 4481 . G . . END=4502 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,106,1289 -20_10037292_10066351 4503 . G . . END=4503 GT:DP:GQ:MIN_DP:PL 0/0:43:67:43:0,67,1218 -20_10037292_10066351 4504 . A . . END=4592 GT:DP:GQ:MIN_DP:PL 0/0:50:99:42:0,99,1431 -20_10037292_10066351 4593 . G . . END=4593 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1440 -20_10037292_10066351 4594 . T . . END=4604 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 4605 . T . . END=4608 GT:DP:GQ:MIN_DP:PL 0/0:36:96:35:0,96,1440 -20_10037292_10066351 4609 . C . . END=4610 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4611 . G . . END=4611 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 4612 . G . . END=4615 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 4616 . G . . END=4616 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,932 -20_10037292_10066351 4617 . T . . END=4622 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 4623 . A . . END=4623 GT:DP:GQ:MIN_DP:PL 0/0:37:85:37:0,85,983 -20_10037292_10066351 4624 . C . . END=4630 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1094 -20_10037292_10066351 4631 . C . . END=4631 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1118 -20_10037292_10066351 4632 . C . . END=4639 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,101,1156 -20_10037292_10066351 4640 . A . . END=4640 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1108 -20_10037292_10066351 4641 . T . . END=4649 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1217 -20_10037292_10066351 4650 . T . . END=4655 GT:DP:GQ:MIN_DP:PL 0/0:38:93:36:0,93,1395 -20_10037292_10066351 4656 . C . . END=4666 GT:DP:GQ:MIN_DP:PL 0/0:33:84:30:0,84,1260 -20_10037292_10066351 4667 . C . . END=4674 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 4675 . A . . END=4682 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1021 -20_10037292_10066351 4683 . G . . END=4683 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1011 -20_10037292_10066351 4684 . A . . END=4684 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1173 -20_10037292_10066351 4685 . G . . END=4685 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1121 -20_10037292_10066351 4686 . C . . END=4690 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,107,1013 -20_10037292_10066351 4691 . G . . END=4691 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,997 -20_10037292_10066351 4692 . C . . END=4704 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,101,1183 -20_10037292_10066351 4705 . A . . END=4706 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1107 -20_10037292_10066351 4707 . A . . END=4718 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,102,1185 -20_10037292_10066351 4719 . T . . END=4719 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1078 -20_10037292_10066351 4720 . A . . END=4724 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 4725 . C . . END=4725 GT:DP:GQ:MIN_DP:PL 0/0:40:81:40:0,81,1101 -20_10037292_10066351 4726 . A . . END=4733 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,101,1155 -20_10037292_10066351 4734 . C . . END=4734 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1188 -20_10037292_10066351 4735 . T . . END=4735 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,103,1187 -20_10037292_10066351 4736 . A . . END=4736 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1108 -20_10037292_10066351 4737 . C . . END=4739 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,99,1188 -20_10037292_10066351 4740 . T . . END=4740 GT:DP:GQ:MIN_DP:PL 0/0:41:94:41:0,94,1197 -20_10037292_10066351 4741 . A . . END=4746 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,105,1575 -20_10037292_10066351 4747 . T . . END=4747 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1082 -20_10037292_10066351 4748 . T . . END=4748 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 4749 . T . . END=4750 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1092 -20_10037292_10066351 4751 . T . . END=4752 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1170 -20_10037292_10066351 4753 . A . . END=4753 GT:DP:GQ:MIN_DP:PL 0/0:35:64:35:0,64,1027 -20_10037292_10066351 4754 . T . . END=4754 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4755 . A . . END=4755 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1112 -20_10037292_10066351 4756 . A . . END=4757 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1575 -20_10037292_10066351 4758 . C . . END=4758 GT:DP:GQ:MIN_DP:PL 0/0:40:73:40:0,73,1197 -20_10037292_10066351 4759 . A . . END=4790 GT:DP:GQ:MIN_DP:PL 0/0:43:99:36:0,102,1163 -20_10037292_10066351 4791 . G . . END=4791 GT:DP:GQ:MIN_DP:PL 0/0:45:83:45:0,83,1299 -20_10037292_10066351 4792 . A . . END=4889 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,100,1187 -20_10037292_10066351 4890 . C . . END=4890 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1215 -20_10037292_10066351 4891 . T . . END=4895 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 4896 . A . . END=4898 GT:DP:GQ:MIN_DP:PL 0/0:39:96:37:0,96,1440 -20_10037292_10066351 4899 . A . . END=4904 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 4905 . A . . END=4912 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,1060 -20_10037292_10066351 4913 . T . . END=4926 GT:DP:GQ:MIN_DP:PL 0/0:33:84:29:0,84,1260 -20_10037292_10066351 4927 . C . . END=4927 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,819 -20_10037292_10066351 4928 . A . . END=4931 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4932 . G . . END=4932 GT:DP:GQ:MIN_DP:PL 0/0:30:67:30:0,67,865 -20_10037292_10066351 4933 . A . . END=4933 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,910 -20_10037292_10066351 4934 . C . . END=4946 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 4947 . A . . END=4949 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4950 . A . . END=4950 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 4951 . T . . END=4957 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4958 . G . . END=4958 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 4959 . A . . END=4967 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1096 -20_10037292_10066351 4968 . A . . END=5026 GT:DP:GQ:MIN_DP:PL 0/0:43:99:36:0,102,1168 -20_10037292_10066351 5027 . C T, 1377.06 . DP=44;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=158400,44 GT:AD:DP:GQ:PL:SB 1/1:0,44,0:44:99:1391,132,0,1391,132,1391:0,0,22,22 -20_10037292_10066351 5028 . C . . END=5204 GT:DP:GQ:MIN_DP:PL 0/0:48:99:38:0,99,1306 -20_10037292_10066351 5205 . A . . END=5205 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1100 -20_10037292_10066351 5206 . A . . END=5211 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,111,1107 -20_10037292_10066351 5212 . A . . END=5212 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1096 -20_10037292_10066351 5213 . T . . END=5226 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1240 -20_10037292_10066351 5227 . G . . END=5227 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1272 -20_10037292_10066351 5228 . G . . END=5362 GT:DP:GQ:MIN_DP:PL 0/0:49:99:38:0,102,1184 -20_10037292_10066351 5363 . T . . END=5363 GT:DP:GQ:MIN_DP:PL 0/0:49:97:49:0,97,1426 -20_10037292_10066351 5364 . G . . END=5373 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,120,1800 -20_10037292_10066351 5374 . T . . END=5374 GT:DP:GQ:MIN_DP:PL 0/0:46:83:46:0,83,1368 -20_10037292_10066351 5375 . G . . END=5388 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,108,1301 -20_10037292_10066351 5389 . T . . END=5389 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1317 -20_10037292_10066351 5390 . G . . END=5417 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,99,1206 -20_10037292_10066351 5418 . A . . END=5422 GT:DP:GQ:MIN_DP:PL 0/0:40:90:39:0,90,1112 -20_10037292_10066351 5423 . C . . END=5430 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,99,1485 -20_10037292_10066351 5431 . T . . END=5431 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1161 -20_10037292_10066351 5432 . T . . END=5439 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1121 -20_10037292_10066351 5440 . T . . END=5440 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 5441 . G . . END=5441 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 5442 . C . . END=5449 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1171 -20_10037292_10066351 5450 . T . . END=5452 GT:DP:GQ:MIN_DP:PL 0/0:35:87:34:0,87,1305 -20_10037292_10066351 5453 . A . . END=5453 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,1064 -20_10037292_10066351 5454 . G . . END=5454 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 5455 . A . . END=5455 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,968 -20_10037292_10066351 5456 . A . . END=5458 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 5459 . A . . END=5459 GT:DP:GQ:MIN_DP:PL 0/0:34:81:34:0,81,1051 -20_10037292_10066351 5460 . A . . END=5460 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,1029 -20_10037292_10066351 5461 . G . . END=5461 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 5462 . A . . END=5462 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,995 -20_10037292_10066351 5463 . T . . END=5464 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5465 . A . . END=5465 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,1030 -20_10037292_10066351 5466 . A . . END=5466 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1025 -20_10037292_10066351 5467 . T . . END=5467 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5468 . G . . END=5468 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5469 . A G, 862.06 . DP=29;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=104400,29 GT:AD:DP:GQ:PL:SB 1/1:0,29,0:29:86:876,86,0,876,86,876:0,0,14,15 -20_10037292_10066351 5470 . G . . END=5470 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,999 -20_10037292_10066351 5471 . C . . END=5471 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5472 . A . . END=5472 GT:DP:GQ:MIN_DP:PL 0/0:34:80:34:0,80,1066 -20_10037292_10066351 5473 . A . . END=5473 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5474 . G . . END=5477 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5478 . A . . END=5478 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,1012 -20_10037292_10066351 5479 . G . . END=5479 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5480 . C . . END=5483 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 5484 . G . . END=5484 GT:DP:GQ:MIN_DP:PL 0/0:33:65:33:0,65,1006 -20_10037292_10066351 5485 . A . . END=5492 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 5493 . T . . END=5493 GT:DP:GQ:MIN_DP:PL 0/0:33:62:33:0,62,918 -20_10037292_10066351 5494 . T . . END=5494 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1017 -20_10037292_10066351 5495 . T . . END=5495 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1098 -20_10037292_10066351 7536 . C . . END=7536 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,103,1287 -20_10037292_10066351 7537 . C . . END=7537 GT:DP:GQ:MIN_DP:PL 0/0:43:85:43:0,85,1165 -20_10037292_10066351 7538 . C . . END=7552 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,102,1206 -20_10037292_10066351 7553 . A . . END=7553 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1289 -20_10037292_10066351 7554 . A . . END=7555 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1162 -20_10037292_10066351 7556 . C . . END=7556 GT:DP:GQ:MIN_DP:PL 0/0:38:69:38:0,69,1008 -20_10037292_10066351 7557 . A G, 996.06 . DP=38;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=136800,38 GT:AD:DP:GQ:PL:SB 1/1:0,37,0:37:99:1010,108,0,1010,108,1010:0,0,16,21 -20_10037292_10066351 7558 . C . . END=7559 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 7560 . C . . END=7560 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1020 -20_10037292_10066351 7561 . G . . END=7561 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 7562 . G . . END=7562 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1124 -20_10037292_10066351 7563 . T . . END=7566 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1575 -20_10037292_10066351 7567 . G . . END=7567 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1137 -20_10037292_10066351 7568 . G . . END=7569 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 7570 . C . . END=7574 GT:DP:GQ:MIN_DP:PL 0/0:37:96:35:0,96,1440 -20_10037292_10066351 7575 . T . . END=7581 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 -20_10037292_10066351 7582 . T . . END=7584 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1170 -20_10037292_10066351 7585 . G . . END=7591 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 7592 . T . . END=7602 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,772 -20_10037292_10066351 7603 . T . . END=7609 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 7610 . G . . END=7610 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 7611 . A . . END=7611 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,994 -20_10037292_10066351 7612 . G . . END=7630 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,991 -20_10037292_10066351 7631 . T . . END=7635 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1054 -20_10037292_10066351 7636 . G . . END=7639 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 7640 . T . . END=7653 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,99,1241 -20_10037292_10066351 7654 . G . . END=7654 GT:DP:GQ:MIN_DP:PL 0/0:41:82:41:0,82,1213 -20_10037292_10066351 7655 . C . . END=7658 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,115,1317 -20_10037292_10066351 7659 . G . . END=7659 GT:DP:GQ:MIN_DP:PL 0/0:43:90:43:0,90,1260 -20_10037292_10066351 7660 . T . . END=7675 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,101,1234 -20_10037292_10066351 7676 . G . . END=7676 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1157 -20_10037292_10066351 7677 . T . . END=7680 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,108,1219 -20_10037292_10066351 7681 . C . . END=7681 GT:DP:GQ:MIN_DP:PL 0/0:40:62:40:0,62,1083 -20_10037292_10066351 7682 . C . . END=7684 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,106,1189 -20_10037292_10066351 7685 . G . . END=7685 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1207 -20_10037292_10066351 7686 . T . . END=7694 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,100,1179 -20_10037292_10066351 7695 . G . . END=7695 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1216 -20_10037292_10066351 7696 . T . . END=7696 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,115,1278 -20_10037292_10066351 7697 . A . . END=7697 GT:DP:GQ:MIN_DP:PL 0/0:42:85:42:0,85,1238 -20_10037292_10066351 7698 . C . . END=7724 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,99,1244 -20_10037292_10066351 7725 . C . . END=7725 GT:DP:GQ:MIN_DP:PL 0/0:44:91:44:0,91,1217 -20_10037292_10066351 7726 . A . . END=7785 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,100,1272 -20_10037292_10066351 7786 . G T, 1380.06 . DP=44;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=158400,44 GT:AD:DP:GQ:PL:SB 1/1:0,44,0:44:99:1394,132,0,1394,132,1394:0,0,22,22 -20_10037292_10066351 7787 . C . . END=7822 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,105,1208 -20_10037292_10066351 7823 . A . . END=7823 GT:DP:GQ:MIN_DP:PL 0/0:45:96:45:0,96,1299 -20_10037292_10066351 7824 . C . . END=7824 GT:DP:GQ:MIN_DP:PL 0/0:45:99:45:0,112,1315 -20_10037292_10066351 7825 . C . . END=7825 GT:DP:GQ:MIN_DP:PL 0/0:44:84:44:0,84,1272 -20_10037292_10066351 7826 . T . . END=7860 GT:DP:GQ:MIN_DP:PL 0/0:42:99:35:0,105,1100 -20_10037292_10066351 7861 . A . . END=7861 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1124 -20_10037292_10066351 7862 . G . . END=7863 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,110,1094 -20_10037292_10066351 7864 . G . . END=7864 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1019 -20_10037292_10066351 7865 . C . . END=7871 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,105,1050 -20_10037292_10066351 7872 . A . . END=7872 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1192 -20_10037292_10066351 7873 . G . . END=7891 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,99,1187 -20_10037292_10066351 7892 . C . . END=7892 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1259 -20_10037292_10066351 7893 . T . . END=7894 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 7895 . C . . END=7895 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1213 -20_10037292_10066351 7896 . C . . END=7899 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1530 -20_10037292_10066351 7900 . T . . END=7904 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1160 -20_10037292_10066351 7905 . C . . END=7908 GT:DP:GQ:MIN_DP:PL 0/0:35:87:34:0,87,1029 -20_10037292_10066351 7909 . T . . END=7909 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 7910 . G . . END=7911 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 -20_10037292_10066351 7912 . A . . END=7912 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,988 -20_10037292_10066351 7913 . C . . END=7931 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,864 -20_10037292_10066351 7932 . A . . END=7932 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,934 -20_10037292_10066351 7933 . T . . END=7933 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,906 -20_10037292_10066351 7934 . A . . END=7934 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,896 -20_10037292_10066351 7935 . G . . END=7935 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,992 -20_10037292_10066351 7936 . G . . END=7936 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,924 -20_10037292_10066351 7937 . G . . END=7937 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,976 -20_10037292_10066351 7938 . G . . END=7939 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 7940 . A . . END=7949 GT:DP:GQ:MIN_DP:PL 0/0:30:72:29:0,72,974 -20_10037292_10066351 7950 . A . . END=7950 GT:DP:GQ:MIN_DP:PL 0/0:31:57:31:0,57,888 -20_10037292_10066351 7951 . A . . END=7956 GT:DP:GQ:MIN_DP:PL 0/0:29:75:27:0,75,1125 -20_10037292_10066351 7957 . T . . END=7957 GT:DP:GQ:MIN_DP:PL 0/0:26:50:26:0,50,787 -20_10037292_10066351 7958 . G . . END=7958 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 7959 . G . . END=7959 GT:DP:GQ:MIN_DP:PL 0/0:25:42:25:0,42,696 -20_10037292_10066351 7960 . T . . END=7960 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 7961 . A . . END=7961 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,824 -20_10037292_10066351 7962 . T . . END=7964 GT:DP:GQ:MIN_DP:PL 0/0:27:72:25:0,72,772 -20_10037292_10066351 7965 . T . . END=7965 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,803 -20_10037292_10066351 7966 . A . . END=7967 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 7968 . C . . END=7998 GT:DP:GQ:MIN_DP:PL 0/0:24:60:22:0,60,900 -20_10037292_10066351 7999 . T . . END=7999 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,730 -20_10037292_10066351 8000 . T . . END=8002 GT:DP:GQ:MIN_DP:PL 0/0:25:67:25:0,67,801 -20_10037292_10066351 8003 . C . . END=8005 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 8006 . A . . END=8037 GT:DP:GQ:MIN_DP:PL 0/0:26:63:23:0,63,713 -20_10037292_10066351 8038 . G . . END=8038 GT:DP:GQ:MIN_DP:PL 0/0:23:57:23:0,57,723 -20_10037292_10066351 8039 . C . . END=8039 GT:DP:GQ:MIN_DP:PL 0/0:22:63:22:0,63,945 -20_10037292_10066351 8040 . A . . END=8040 GT:DP:GQ:MIN_DP:PL 0/0:22:44:22:0,44,674 -20_10037292_10066351 8041 . T . . END=8044 GT:DP:GQ:MIN_DP:PL 0/0:22:63:22:0,63,675 -20_10037292_10066351 8045 . G . . END=8045 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,771 -20_10037292_10066351 8046 . C . . END=8050 GT:DP:GQ:MIN_DP:PL 0/0:25:66:23:0,66,799 -20_10037292_10066351 8051 . C . . END=8061 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,1080 -20_10037292_10066351 8062 . C . . END=8063 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 -20_10037292_10066351 8064 . G . . END=8064 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8065 . C . . END=8065 GT:DP:GQ:MIN_DP:PL 0/0:25:61:25:0,61,727 -20_10037292_10066351 8066 . A . . END=8066 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8067 . A . . END=8067 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,727 -20_10037292_10066351 8068 . G . . END=8068 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8069 . T . . END=8069 GT:DP:GQ:MIN_DP:PL 0/0:26:64:26:0,64,763 -20_10037292_10066351 8070 . G . . END=8075 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8076 . A . . END=8076 GT:DP:GQ:MIN_DP:PL 0/0:25:63:25:0,63,723 -20_10037292_10066351 8077 . A . . END=8078 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8079 . G . . END=8079 GT:DP:GQ:MIN_DP:PL 0/0:23:69:23:0,69,704 -20_10037292_10066351 8080 . C . . END=8086 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,671 -20_10037292_10066351 8087 . A . . END=8087 GT:DP:GQ:MIN_DP:PL 0/0:26:67:26:0,67,782 -20_10037292_10066351 8088 . C . . END=8088 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8089 . A . . END=8089 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,783 -20_10037292_10066351 8090 . A . . END=8090 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8091 . G . . END=8091 GT:DP:GQ:MIN_DP:PL 0/0:29:62:29:0,62,814 -20_10037292_10066351 8092 . A . . END=8095 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,785 -20_10037292_10066351 8096 . A . . END=8102 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,899 -20_10037292_10066351 8103 . A . . END=8104 GT:DP:GQ:MIN_DP:PL 0/0:31:63:30:0,63,870 -20_10037292_10066351 8105 . A . . END=8106 GT:DP:GQ:MIN_DP:PL 0/0:31:74:30:0,74,895 -20_10037292_10066351 8107 . G . . END=8113 GT:DP:GQ:MIN_DP:PL 0/0:31:87:29:0,87,890 -20_10037292_10066351 8114 . G . . END=8114 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,967 -20_10037292_10066351 8115 . A . . END=8115 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 8116 . A . . END=8117 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,851 -20_10037292_10066351 8118 . A . . END=8119 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 8120 . A . . END=8124 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8125 . A . . END=8125 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,969 -20_10037292_10066351 8126 . A . . END=8129 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,985 -20_10037292_10066351 8130 . C . . END=8131 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8132 . C . . END=8134 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8135 . C . . END=8142 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,1215 -20_10037292_10066351 8143 . G . . END=8151 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8152 . G . . END=8154 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1079 -20_10037292_10066351 8155 . A . . END=8155 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1065 -20_10037292_10066351 8156 . A . . END=8160 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,105,1122 -20_10037292_10066351 8161 . A . . END=8161 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1108 -20_10037292_10066351 8162 . T . . END=8179 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,101,1124 -20_10037292_10066351 8180 . G . . END=8180 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1035 -20_10037292_10066351 8181 . A . . END=8181 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1088 -20_10037292_10066351 8182 . T . . END=8182 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,995 -20_10037292_10066351 8183 . T . . END=8183 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1016 -20_10037292_10066351 8184 . T . . END=8206 GT:DP:GQ:MIN_DP:PL 0/0:40:99:33:0,99,1046 -20_10037292_10066351 8207 . C . . END=8207 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1199 -20_10037292_10066351 8208 . C . . END=8247 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,111,1280 -20_10037292_10066351 8248 . T . . END=8248 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1108 -20_10037292_10066351 8249 . T . . END=8325 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,99,1177 -20_10037292_10066351 8326 . G . . END=8326 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1231 -20_10037292_10066351 8327 . A . . END=8333 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,105,1575 -20_10037292_10066351 8334 . A . . END=8334 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1440 -20_10037292_10066351 8335 . A . . END=8336 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,99,1485 -20_10037292_10066351 8337 . A . . END=8339 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1395 -20_10037292_10066351 8340 . T . . END=8349 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,99,1485 -20_10037292_10066351 8350 . G C, 1132.06 . DP=36;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=129600,36 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:1146,108,0,1146,108,1146:0,0,16,20 -20_10037292_10066351 8351 . A . . END=8354 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1160 -20_10037292_10066351 8355 . C . . END=8355 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1106 -20_10037292_10066351 8356 . T . . END=8391 GT:DP:GQ:MIN_DP:PL 0/0:37:99:33:0,99,1042 -20_10037292_10066351 8392 . T . . END=8392 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1069 -20_10037292_10066351 8393 . G . . END=8393 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8394 . G . . END=8394 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8395 . A . . END=8395 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1105 -20_10037292_10066351 8396 . G . . END=8396 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8397 . G . . END=8397 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1084 -20_10037292_10066351 8398 . C . . END=8398 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 8399 . A . . END=8407 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 8408 . T . . END=8408 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,1047 -20_10037292_10066351 8409 . C . . END=8409 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8410 . C . . END=8410 GT:DP:GQ:MIN_DP:PL 0/0:34:51:34:0,51,981 -20_10037292_10066351 8411 . C . . END=8411 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 8412 . T . . END=8422 GT:DP:GQ:MIN_DP:PL 0/0:30:75:28:0,75,1125 -20_10037292_10066351 8423 . T . . END=8425 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8426 . C . . END=8433 GT:DP:GQ:MIN_DP:PL 0/0:29:74:28:0,74,918 -20_10037292_10066351 8434 . T . . END=8434 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8435 . G . . END=8439 GT:DP:GQ:MIN_DP:PL 0/0:30:72:28:0,72,1080 -20_10037292_10066351 8440 . C . . END=8440 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,857 -20_10037292_10066351 8441 . T . . END=8449 GT:DP:GQ:MIN_DP:PL 0/0:28:70:27:0,70,761 -20_10037292_10066351 8450 . C . . END=8450 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,821 -20_10037292_10066351 8451 . A . . END=8453 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 8454 . G . . END=8454 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,750 -20_10037292_10066351 8455 . T . . END=8456 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8457 . T . . END=8458 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,872 -20_10037292_10066351 8459 . G . . END=8460 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,912 -20_10037292_10066351 8461 . T . . END=8461 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,904 -20_10037292_10066351 8462 . C . . END=8462 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,846 -20_10037292_10066351 8463 . C . . END=8471 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,898 -20_10037292_10066351 8472 . C . . END=8472 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8473 . T . . END=8473 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,911 -20_10037292_10066351 8474 . C . . END=8479 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,900 -20_10037292_10066351 8480 . G . . END=8480 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8481 . G . . END=8483 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8484 . T . . END=8484 GT:DP:GQ:MIN_DP:PL 0/0:31:68:31:0,68,872 -20_10037292_10066351 8485 . T . . END=8490 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 8491 . G . . END=8491 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,744 -20_10037292_10066351 8492 . T . . END=8493 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 8494 . T . . END=8494 GT:DP:GQ:MIN_DP:PL 0/0:28:54:28:0,54,774 -20_10037292_10066351 8495 . G . . END=8496 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 8497 . G . . END=8497 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,759 -20_10037292_10066351 8498 . C . . END=8498 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,781 -20_10037292_10066351 8499 . T . . END=8502 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,780 -20_10037292_10066351 8503 . A . . END=8503 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,780 -20_10037292_10066351 8504 . C . . END=8514 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 8515 . A . . END=8520 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 8521 . C . . END=8525 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 8526 . A . . END=8526 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1049 -20_10037292_10066351 8527 . T . . END=8586 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1078 -20_10037292_10066351 8587 . C . . END=8587 GT:DP:GQ:MIN_DP:PL 0/0:39:68:39:0,68,1117 -20_10037292_10066351 8588 . C . . END=8589 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 8590 . G . . END=8590 GT:DP:GQ:MIN_DP:PL 0/0:39:85:39:0,85,1204 -20_10037292_10066351 8591 . C . . END=8591 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 8592 . T . . END=8592 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1174 -20_10037292_10066351 8593 . G . . END=8594 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,105,1085 -20_10037292_10066351 8595 . T . . END=8595 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1078 -20_10037292_10066351 8596 . C . . END=8596 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8597 . C . . END=8599 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8600 . T . . END=8600 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 8601 . G . . END=8601 GT:DP:GQ:MIN_DP:PL 0/0:36:82:36:0,82,1089 -20_10037292_10066351 8602 . A . . END=8604 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 8605 . A . . END=8615 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 8616 . A . . END=8616 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,992 -20_10037292_10066351 8617 . C . . END=8621 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1172 -20_10037292_10066351 8622 . A . . END=8622 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1142 -20_10037292_10066351 8623 . A . . END=8626 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1161 -20_10037292_10066351 8627 . T . . END=8627 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1107 -20_10037292_10066351 8628 . C . . END=8633 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1183 -20_10037292_10066351 8634 . T . . END=8634 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1029 -20_10037292_10066351 8635 . G . . END=8638 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,101,1091 -20_10037292_10066351 8639 . C . . END=8640 GT:DP:GQ:MIN_DP:PL 0/0:39:87:38:0,87,1121 -20_10037292_10066351 8641 . A . . END=8646 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,102,1530 -20_10037292_10066351 8647 . T . . END=8647 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1107 -20_10037292_10066351 8648 . T . . END=8648 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 8649 . T . . END=8649 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1060 -20_10037292_10066351 8650 . C . . END=8650 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1122 -20_10037292_10066351 8651 . T . . END=8652 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 8653 . C . . END=8654 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1051 -20_10037292_10066351 8655 . C . . END=8656 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 8657 . C . . END=8657 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,997 -20_10037292_10066351 8658 . C . . END=8658 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8659 . A . . END=8659 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8660 . G . . END=8660 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,990 -20_10037292_10066351 8661 . T . . END=8662 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1018 -20_10037292_10066351 8663 . A . . END=8667 GT:DP:GQ:MIN_DP:PL 0/0:38:93:36:0,93,1065 -20_10037292_10066351 8668 . A . . END=8679 GT:DP:GQ:MIN_DP:PL 0/0:32:82:31:0,82,918 -20_10037292_10066351 8680 . A . . END=8681 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 8682 . G . . END=8684 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8685 . T . . END=8685 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,762 -20_10037292_10066351 8686 . C . . END=8687 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8688 . G . . END=8688 GT:DP:GQ:MIN_DP:PL 0/0:32:61:32:0,61,872 -20_10037292_10066351 8689 . A . . END=8691 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,834 -20_10037292_10066351 8692 . G . . END=8698 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,868 -20_10037292_10066351 8699 . T . . END=8701 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8702 . T . . END=8703 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8704 . T . . END=8704 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8705 . T . . END=8705 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 8706 . G . . END=8706 GT:DP:GQ:MIN_DP:PL 0/0:35:77:35:0,77,957 -20_10037292_10066351 8707 . T . . END=8709 GT:DP:GQ:MIN_DP:PL 0/0:35:96:33:0,96,1440 -20_10037292_10066351 8710 . G . . END=8710 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,997 -20_10037292_10066351 8711 . C . . END=8712 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 8713 . C . . END=8714 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8715 . T . . END=8718 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8719 . T . . END=8721 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1045 -20_10037292_10066351 8722 . G . . END=8722 GT:DP:GQ:MIN_DP:PL 0/0:36:61:36:0,61,992 -20_10037292_10066351 8723 . G . . END=8727 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 8728 . G . . END=8728 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,990 -20_10037292_10066351 8729 . A . . END=8729 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 8730 . G . . END=8730 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,969 -20_10037292_10066351 8731 . T . . END=8734 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,913 -20_10037292_10066351 8735 . T . . END=8739 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,975 -20_10037292_10066351 8740 . C . . END=8740 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,927 -20_10037292_10066351 8741 . C . . END=8743 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,967 -20_10037292_10066351 8744 . A . . END=8744 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,923 -20_10037292_10066351 8745 . A . . END=8745 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,890 -20_10037292_10066351 8746 . C . . END=8748 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8749 . C . . END=8750 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,994 -20_10037292_10066351 8751 . G . . END=8759 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,103,1064 -20_10037292_10066351 8760 . T . . END=8760 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1017 -20_10037292_10066351 8761 . T . . END=8762 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1096 -20_10037292_10066351 8763 . T . . END=8763 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1001 -20_10037292_10066351 8764 . A . . END=8765 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 8766 . A . . END=8766 GT:DP:GQ:MIN_DP:PL 0/0:38:89:38:0,89,1145 -20_10037292_10066351 8767 . G . . END=8767 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 8768 . G . . END=8768 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1150 -20_10037292_10066351 8769 . T . . END=8769 GT:DP:GQ:MIN_DP:PL 0/0:39:77:39:0,77,999 -20_10037292_10066351 8770 . G . . END=8773 GT:DP:GQ:MIN_DP:PL 0/0:37:91:36:0,91,1016 -20_10037292_10066351 8774 . G . . END=8774 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 8775 . C . . END=8775 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,998 -20_10037292_10066351 8776 . T . . END=8778 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,104,1072 -20_10037292_10066351 8779 . C . . END=8779 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1068 -20_10037292_10066351 8780 . A . . END=8781 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,113,1260 -20_10037292_10066351 8782 . G . . END=8782 GT:DP:GQ:MIN_DP:PL 0/0:42:59:42:0,59,1161 -20_10037292_10066351 8783 . A . . END=8787 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,117,1755 -20_10037292_10066351 8788 . G . . END=8788 GT:DP:GQ:MIN_DP:PL 0/0:41:75:41:0,75,1144 -20_10037292_10066351 8789 . T . . END=8789 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,937 -20_10037292_10066351 8790 . A . . END=8790 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,117,1755 -20_10037292_10066351 8791 . G . . END=8791 GT:DP:GQ:MIN_DP:PL 0/0:43:55:43:0,55,1222 -20_10037292_10066351 8792 . G . . END=8792 GT:DP:GQ:MIN_DP:PL 0/0:42:90:42:0,90,1152 -20_10037292_10066351 8793 . G . . END=8794 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,113,1282 -20_10037292_10066351 8795 . T . . END=8795 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1048 -20_10037292_10066351 8796 . T . . END=8800 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,99,1149 -20_10037292_10066351 8801 . T . . END=8802 GT:DP:GQ:MIN_DP:PL 0/0:44:92:44:0,92,1165 -20_10037292_10066351 8803 . C . . END=8804 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,109,1257 -20_10037292_10066351 8805 . C . . END=8805 GT:DP:GQ:MIN_DP:PL 0/0:43:80:43:0,80,1124 -20_10037292_10066351 8806 . C . . END=8813 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,101,1225 -20_10037292_10066351 8814 . G . . END=8814 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1205 -20_10037292_10066351 8815 . A . . END=8816 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,120,1800 -20_10037292_10066351 8817 . T . . END=8817 GT:DP:GQ:MIN_DP:PL 0/0:42:60:42:0,60,818 -20_10037292_10066351 8818 . T . . END=8818 GT:DP:GQ:MIN_DP:PL 0/0:41:81:41:0,81,952 -20_10037292_10066351 8819 . A . . END=8825 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,108,1206 -20_10037292_10066351 8826 . C . . END=8827 GT:DP:GQ:MIN_DP:PL 0/0:41:73:41:0,73,968 -20_10037292_10066351 8828 . G . . END=8832 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,104,1214 -20_10037292_10066351 8833 . G . . END=8833 GT:DP:GQ:MIN_DP:PL 0/0:39:79:39:0,79,1094 -20_10037292_10066351 8834 . G . . END=8834 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 8835 . C . . END=8835 GT:DP:GQ:MIN_DP:PL 0/0:40:77:40:0,77,982 -20_10037292_10066351 8836 . A . . END=8836 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,120,1800 -20_10037292_10066351 8837 . G . . END=8837 GT:DP:GQ:MIN_DP:PL 0/0:43:83:43:0,83,1211 -20_10037292_10066351 8838 . A . . END=8840 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,120,1800 -20_10037292_10066351 8841 . G . . END=8841 GT:DP:GQ:MIN_DP:PL 0/0:42:64:42:0,64,1114 -20_10037292_10066351 8842 . A . . END=8842 GT:DP:GQ:MIN_DP:PL 0/0:42:95:42:0,95,1237 -20_10037292_10066351 8843 . A . . END=8845 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,114,1710 -20_10037292_10066351 8846 . G . . END=8846 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1210 -20_10037292_10066351 8847 . G . . END=8851 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,100,1214 -20_10037292_10066351 8852 . G . . END=8852 GT:DP:GQ:MIN_DP:PL 0/0:41:88:41:0,88,1155 -20_10037292_10066351 8853 . G . . END=8853 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1143 -20_10037292_10066351 8854 . A . . END=8860 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,105,1575 -20_10037292_10066351 8861 . A . . END=8861 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1254 -20_10037292_10066351 8862 . G . . END=8863 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,108,1620 -20_10037292_10066351 8864 . G . . END=8864 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,1056 -20_10037292_10066351 8865 . G . . END=8869 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1130 -20_10037292_10066351 8870 . G . . END=8870 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1042 -20_10037292_10066351 8871 . G . . END=8871 GT:DP:GQ:MIN_DP:PL 0/0:35:59:35:0,59,927 -20_10037292_10066351 8872 . A . . END=8880 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 8881 . A . . END=8885 GT:DP:GQ:MIN_DP:PL 0/0:38:81:37:0,81,1215 -20_10037292_10066351 8886 . AAGAAAGAAAG A, 951.03 . DP=30;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=108000,30 GT:AD:DP:GQ:PL:SB 1/1:0,22,0:22:67:965,67,0,965,67,965:0,0,20,2 -20_10037292_10066351 8897 . A . . END=8903 GT:DP:GQ:MIN_DP:PL 0/0:34:84:31:0,84,1260 -20_10037292_10066351 8904 . A . . END=8904 GT:DP:GQ:MIN_DP:PL 0/0:31:0:31:0,0,722 -20_10037292_10066351 8905 . A . . END=8905 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8906 . G . . END=8906 GT:DP:GQ:MIN_DP:PL 0/0:32:4:32:0,4,766 -20_10037292_10066351 8907 . A . . END=8908 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8909 . A . . END=8912 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,933 -20_10037292_10066351 8913 . A . . END=8913 GT:DP:GQ:MIN_DP:PL 0/0:31:82:31:0,82,920 -20_10037292_10066351 8914 . G . . END=8914 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,908 -20_10037292_10066351 8915 . A . . END=8916 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 8917 . A . . END=8917 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8918 . G . . END=8918 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,873 -20_10037292_10066351 8919 . A . . END=8920 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 8921 . A . . END=8921 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,889 -20_10037292_10066351 8922 . G . . END=8928 GT:DP:GQ:MIN_DP:PL 0/0:32:75:32:0,75,1125 -20_10037292_10066351 8929 . G . . END=8929 GT:DP:GQ:MIN_DP:PL 0/0:31:67:31:0,67,862 -20_10037292_10066351 8930 . A . . END=8936 GT:DP:GQ:MIN_DP:PL 0/0:33:71:30:0,71,953 -20_10037292_10066351 8937 . G . . END=8937 GT:DP:GQ:MIN_DP:PL 0/0:31:33:31:0,33,805 -20_10037292_10066351 8938 . A . . END=8938 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 8939 . G . . END=8939 GT:DP:GQ:MIN_DP:PL 0/0:28:38:28:0,38,740 -20_10037292_10066351 8940 . A . . END=8941 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 8942 . A . . END=8942 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,1035 -20_10037292_10066351 8943 . G . . END=8943 GT:DP:GQ:MIN_DP:PL 0/0:28:36:28:0,36,696 -20_10037292_10066351 8944 . A . . END=8947 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,727 -20_10037292_10066351 8948 . G . . END=8948 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,740 -20_10037292_10066351 8949 . G . . END=8949 GT:DP:GQ:MIN_DP:PL 0/0:27:41:27:0,41,632 -20_10037292_10066351 8950 . A . . END=8951 GT:DP:GQ:MIN_DP:PL 0/0:27:69:26:0,69,1035 -20_10037292_10066351 8952 . A . . END=8953 GT:DP:GQ:MIN_DP:PL 0/0:25:59:25:0,59,671 -20_10037292_10066351 8954 . A . . END=8954 GT:DP:GQ:MIN_DP:PL 0/0:25:66:25:0,66,990 -20_10037292_10066351 8955 . G . . END=8955 GT:DP:GQ:MIN_DP:PL 0/0:25:49:25:0,49,649 -20_10037292_10066351 8956 . A . . END=8957 GT:DP:GQ:MIN_DP:PL 0/0:27:65:26:0,65,792 -20_10037292_10066351 8958 . A . . END=8958 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8959 . G . . END=8959 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,823 -20_10037292_10066351 8960 . A . . END=8962 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8963 . G . . END=8963 GT:DP:GQ:MIN_DP:PL 0/0:28:51:28:0,51,765 -20_10037292_10066351 8964 . A . . END=8964 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8965 . G . . END=8965 GT:DP:GQ:MIN_DP:PL 0/0:28:52:28:0,52,736 -20_10037292_10066351 8966 . A . . END=8967 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8968 . G . . END=8968 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,792 -20_10037292_10066351 8969 . G . . END=8969 GT:DP:GQ:MIN_DP:PL 0/0:28:25:28:0,25,733 -20_10037292_10066351 8970 . A . . END=8974 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8975 . G . . END=8975 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,755 -20_10037292_10066351 8976 . A . . END=8976 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 8977 . G . . END=8977 GT:DP:GQ:MIN_DP:PL 0/0:29:54:29:0,54,794 -20_10037292_10066351 8978 . A . . END=8981 GT:DP:GQ:MIN_DP:PL 0/0:29:74:28:0,74,898 -20_10037292_10066351 8982 . A . . END=8982 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8983 . G . . END=8983 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,858 -20_10037292_10066351 8984 . A . . END=8988 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8989 . G . . END=8989 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,829 -20_10037292_10066351 8990 . A . . END=8992 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8993 . G . . END=8993 GT:DP:GQ:MIN_DP:PL 0/0:32:51:32:0,51,788 -20_10037292_10066351 8994 . A . . END=8994 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8995 . G . . END=8995 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,844 -20_10037292_10066351 8996 . A . . END=8996 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8997 . G . . END=8997 GT:DP:GQ:MIN_DP:PL 0/0:32:41:32:0,41,828 -20_10037292_10066351 8998 . A . . END=8998 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8999 . G . . END=8999 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,719 -20_10037292_10066351 9000 . A . . END=9002 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 9003 . G . . END=9003 GT:DP:GQ:MIN_DP:PL 0/0:33:24:33:0,24,806 -20_10037292_10066351 9004 . A . . END=9006 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,1125 -20_10037292_10066351 9007 . G . . END=9007 GT:DP:GQ:MIN_DP:PL 0/0:34:32:34:0,32,867 -20_10037292_10066351 9008 . G . . END=9010 GT:DP:GQ:MIN_DP:PL 0/0:34:70:33:0,70,904 -20_10037292_10066351 9011 . G . . END=9011 GT:DP:GQ:MIN_DP:PL 0/0:34:48:34:0,48,883 -20_10037292_10066351 9012 . G . . END=9012 GT:DP:GQ:MIN_DP:PL 0/0:35:57:35:0,57,916 -20_10037292_10066351 9013 . A . . END=9014 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 9015 . G . . END=9015 GT:DP:GQ:MIN_DP:PL 0/0:32:47:32:0,47,817 -20_10037292_10066351 9016 . G . . END=9018 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 9019 . G . . END=9019 GT:DP:GQ:MIN_DP:PL 0/0:31:17:31:0,17,656 -20_10037292_10066351 9020 . A . . END=9023 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,830 -20_10037292_10066351 9024 . A . . END=9024 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,908 -20_10037292_10066351 9025 . T . . END=9025 GT:DP:GQ:MIN_DP:PL 0/0:31:0:31:0,0,565 -20_10037292_10066351 9026 . G . . END=9026 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,793 -20_10037292_10066351 9027 . A . . END=9028 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,910 -20_10037292_10066351 9029 . G . . END=9029 GT:DP:GQ:MIN_DP:PL 0/0:31:35:31:0,35,751 -20_10037292_10066351 9030 . G . . END=9030 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,788 -20_10037292_10066351 9031 . G . . END=9031 GT:DP:GQ:MIN_DP:PL 0/0:31:48:31:0,48,740 -20_10037292_10066351 9032 . A . . END=9032 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,957 -20_10037292_10066351 9033 . G . . END=9033 GT:DP:GQ:MIN_DP:PL 0/0:31:7:31:0,7,679 -20_10037292_10066351 9034 . G . . END=9034 GT:DP:GQ:MIN_DP:PL 0/0:30:47:30:0,47,734 -20_10037292_10066351 9035 . A . . END=9035 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 9036 . A . . END=9036 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 9037 . G . . END=9037 GT:DP:GQ:MIN_DP:PL 0/0:31:18:31:0,18,704 -20_10037292_10066351 9038 . G . . END=9038 GT:DP:GQ:MIN_DP:PL 0/0:30:8:30:0,8,670 -20_10037292_10066351 9039 . A . . END=9043 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 9044 . G . . END=9044 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,924 -20_10037292_10066351 9045 . G . . END=9046 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9047 . G . . END=9047 GT:DP:GQ:MIN_DP:PL 0/0:28:62:28:0,62,781 -20_10037292_10066351 9048 . A . . END=9048 GT:DP:GQ:MIN_DP:PL 0/0:29:76:29:0,76,828 -20_10037292_10066351 9049 . C . . END=9049 GT:DP:GQ:MIN_DP:PL 0/0:29:59:29:0,59,696 -20_10037292_10066351 9050 . A . . END=9050 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 9051 . G . . END=9051 GT:DP:GQ:MIN_DP:PL 0/0:29:68:29:0,68,812 -20_10037292_10066351 9052 . G . . END=9052 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9053 . A . . END=9053 GT:DP:GQ:MIN_DP:PL 0/0:31:72:31:0,72,916 -20_10037292_10066351 9054 . A . . END=9054 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9055 . G . . END=9055 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,853 -20_10037292_10066351 9056 . G . . END=9056 GT:DP:GQ:MIN_DP:PL 0/0:32:56:32:0,56,834 -20_10037292_10066351 9057 . A . . END=9058 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 9059 . G . . END=9059 GT:DP:GQ:MIN_DP:PL 0/0:35:49:35:0,49,882 -20_10037292_10066351 9060 . A . . END=9062 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 9063 . G . . END=9063 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,966 -20_10037292_10066351 9064 . A . . END=9066 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9067 . A . . END=9067 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1111 -20_10037292_10066351 9068 . A . . END=9068 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,103,1210 -20_10037292_10066351 9069 . G . . END=9070 GT:DP:GQ:MIN_DP:PL 0/0:38:95:37:0,95,1130 -20_10037292_10066351 9071 . A . . END=9071 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9072 . G . . END=9072 GT:DP:GQ:MIN_DP:PL 0/0:39:72:39:0,72,1096 -20_10037292_10066351 9073 . A . . END=9076 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1575 -20_10037292_10066351 9077 . A . . END=9077 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1122 -20_10037292_10066351 9078 . A . . END=9078 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9079 . G . . END=9079 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1129 -20_10037292_10066351 9080 . A . . END=9081 GT:DP:GQ:MIN_DP:PL 0/0:37:94:36:0,94,1155 -20_10037292_10066351 9082 . A . . END=9082 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9083 . G . . END=9084 GT:DP:GQ:MIN_DP:PL 0/0:38:97:37:0,97,1128 -20_10037292_10066351 9085 . G . . END=9086 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,104,1191 -20_10037292_10066351 9087 . A . . END=9087 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1178 -20_10037292_10066351 9088 . A . . END=9089 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 9090 . A . . END=9090 GT:DP:GQ:MIN_DP:PL 0/0:40:75:40:0,75,1127 -20_10037292_10066351 9091 . A . . END=9093 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 9094 . G . . END=9094 GT:DP:GQ:MIN_DP:PL 0/0:40:70:40:0,70,1129 -20_10037292_10066351 9095 . A . . END=9095 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1152 -20_10037292_10066351 9096 . A . . END=9097 GT:DP:GQ:MIN_DP:PL 0/0:40:73:40:0,73,1129 -20_10037292_10066351 9098 . G . . END=9099 GT:DP:GQ:MIN_DP:PL 0/0:40:88:39:0,88,1119 -20_10037292_10066351 9100 . A . . END=9100 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 9101 . A . . END=9102 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 9103 . A . . END=9103 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1107 -20_10037292_10066351 9104 . A . . END=9109 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 9110 . G . . END=9110 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1156 -20_10037292_10066351 9111 . A . . END=9111 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 9112 . A . . END=9112 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,1075 -20_10037292_10066351 9113 . G . . END=9115 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,101,1235 -20_10037292_10066351 9116 . A . . END=9116 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1139 -20_10037292_10066351 9117 . A . . END=9140 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1026 -20_10037292_10066351 9141 . A . . END=9151 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1091 -20_10037292_10066351 9152 . C . . END=9153 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 9154 . A . . END=9155 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9156 . A . . END=9156 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,954 -20_10037292_10066351 9157 . A . . END=9157 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 9158 . C . . END=9163 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,921 -20_10037292_10066351 9164 . C . . END=9164 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1007 -20_10037292_10066351 9165 . C . . END=9165 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,961 -20_10037292_10066351 9166 . T . . END=9168 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9169 . C . . END=9169 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,934 -20_10037292_10066351 9170 . C . . END=9170 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 9171 . A . . END=9171 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,995 -20_10037292_10066351 9172 . T . . END=9174 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 9175 . A . . END=9175 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,940 -20_10037292_10066351 9176 . A . . END=9176 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1037 -20_10037292_10066351 9177 . T . . END=9177 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,1003 -20_10037292_10066351 9178 . G . . END=9181 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,871 -20_10037292_10066351 9182 . G . . END=9182 GT:DP:GQ:MIN_DP:PL 0/0:32:57:32:0,57,895 -20_10037292_10066351 9183 . A . . END=9184 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1006 -20_10037292_10066351 9185 . T . . END=9185 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1095 -20_10037292_10066351 9186 . T . . END=9186 GT:DP:GQ:MIN_DP:PL 0/0:35:70:35:0,70,1024 -20_10037292_10066351 9187 . T . . END=9188 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 9189 . T . . END=9189 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1048 -20_10037292_10066351 9190 . C . . END=9193 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 9194 . A . . END=9194 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1071 -20_10037292_10066351 9195 . C . . END=9196 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9197 . C . . END=9197 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 9198 . A . . END=9206 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 9207 . C . . END=9208 GT:DP:GQ:MIN_DP:PL 0/0:36:92:35:0,92,1103 -20_10037292_10066351 9209 . T . . END=9209 GT:DP:GQ:MIN_DP:PL 0/0:35:63:35:0,63,1038 -20_10037292_10066351 9210 . T . . END=9211 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 9212 . A . . END=9214 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 -20_10037292_10066351 9215 . T . . END=9219 GT:DP:GQ:MIN_DP:PL 0/0:34:78:32:0,78,1170 -20_10037292_10066351 9220 . C . . END=9222 GT:DP:GQ:MIN_DP:PL 0/0:32:81:29:0,81,1215 -20_10037292_10066351 9223 . C . . END=9224 GT:DP:GQ:MIN_DP:PL 0/0:30:75:29:0,75,1125 -20_10037292_10066351 9225 . A . . END=9227 GT:DP:GQ:MIN_DP:PL 0/0:29:63:27:0,63,945 -20_10037292_10066351 9228 . T . . END=9231 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,1080 -20_10037292_10066351 9232 . C . . END=9232 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,940 -20_10037292_10066351 9233 . C . . END=9236 GT:DP:GQ:MIN_DP:PL 0/0:29:75:26:0,75,832 -20_10037292_10066351 9237 . G . . END=9237 GT:DP:GQ:MIN_DP:PL 0/0:26:62:26:0,62,795 -20_10037292_10066351 9238 . C . . END=9241 GT:DP:GQ:MIN_DP:PL 0/0:27:80:27:0,80,780 -20_10037292_10066351 9242 . C . . END=9243 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,820 -20_10037292_10066351 9244 . C . . END=9244 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,798 -20_10037292_10066351 9245 . A . . END=9248 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 9249 . G . . END=9249 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,874 -20_10037292_10066351 9250 . C . . END=9250 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,912 -20_10037292_10066351 9251 . A . . END=9254 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9255 . T . . END=9255 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,894 -20_10037292_10066351 9256 . C . . END=9257 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9258 . C . . END=9264 GT:DP:GQ:MIN_DP:PL 0/0:28:70:27:0,70,861 -20_10037292_10066351 9265 . A . . END=9265 GT:DP:GQ:MIN_DP:PL 0/0:27:52:27:0,52,775 -20_10037292_10066351 9266 . T . . END=9274 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 9275 . C . . END=9275 GT:DP:GQ:MIN_DP:PL 0/0:26:47:26:0,47,781 -20_10037292_10066351 9276 . A . . END=9282 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9283 . T . . END=9283 GT:DP:GQ:MIN_DP:PL 0/0:29:61:29:0,61,866 -20_10037292_10066351 9284 . C . . END=9284 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 9285 . T . . END=9286 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,888 -20_10037292_10066351 9287 . A . . END=9292 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 9293 . A . . END=9294 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,958 -20_10037292_10066351 9295 . T . . END=9299 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 9300 . T . . END=9300 GT:DP:GQ:MIN_DP:PL 0/0:32:74:32:0,74,931 -20_10037292_10066351 9301 . C . . END=9305 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 9306 . A . . END=9306 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,949 -20_10037292_10066351 9307 . A . . END=9308 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9309 . C . . END=9309 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,886 -20_10037292_10066351 9310 . C . . END=9315 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,943 -20_10037292_10066351 9316 . A . . END=9316 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,941 -20_10037292_10066351 9317 . A . . END=9317 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,978 -20_10037292_10066351 9318 . A . . END=9318 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,959 -20_10037292_10066351 9319 . C . . END=9322 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,997 -20_10037292_10066351 9323 . T . . END=9323 GT:DP:GQ:MIN_DP:PL 0/0:31:48:31:0,48,899 -20_10037292_10066351 9324 . C . . END=9324 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1109 -20_10037292_10066351 9325 . T . . END=9329 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1099 -20_10037292_10066351 9330 . A . . END=9338 GT:DP:GQ:MIN_DP:PL 0/0:35:81:32:0,81,1215 -20_10037292_10066351 9339 . A . . END=9341 GT:DP:GQ:MIN_DP:PL 0/0:31:78:29:0,78,1170 -20_10037292_10066351 9342 . A . . END=9343 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9344 . T . . END=9346 GT:DP:GQ:MIN_DP:PL 0/0:30:78:29:0,78,1170 -20_10037292_10066351 9347 . T . . END=9352 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 9353 . T . . END=9353 GT:DP:GQ:MIN_DP:PL 0/0:28:63:28:0,63,794 -20_10037292_10066351 9354 . T . . END=9360 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 9361 . G . . END=9364 GT:DP:GQ:MIN_DP:PL 0/0:29:71:27:0,71,893 -20_10037292_10066351 9365 . C . . END=9371 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,843 -20_10037292_10066351 9372 . T . . END=9372 GT:DP:GQ:MIN_DP:PL 0/0:29:63:29:0,63,824 -20_10037292_10066351 9373 . C . . END=9376 GT:DP:GQ:MIN_DP:PL 0/0:29:84:28:0,84,882 -20_10037292_10066351 9377 . A . . END=9377 GT:DP:GQ:MIN_DP:PL 0/0:31:69:31:0,69,880 -20_10037292_10066351 9378 . A . . END=9378 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 9379 . T . . END=9379 GT:DP:GQ:MIN_DP:PL 0/0:29:63:29:0,63,880 -20_10037292_10066351 9380 . T . . END=9380 GT:DP:GQ:MIN_DP:PL 0/0:30:56:30:0,56,834 -20_10037292_10066351 9381 . C . . END=9382 GT:DP:GQ:MIN_DP:PL 0/0:30:87:29:0,87,927 -20_10037292_10066351 9383 . C . . END=9383 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,991 -20_10037292_10066351 9384 . A . . END=9385 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1005 -20_10037292_10066351 9386 . A . . END=9386 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 9387 . T . . END=9387 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,989 -20_10037292_10066351 9388 . C . . END=9390 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,979 -20_10037292_10066351 9391 . A . . END=9391 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,925 -20_10037292_10066351 9392 . C . . END=9392 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,969 -20_10037292_10066351 9393 . T . . END=9394 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9395 . T . . END=9396 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,967 -20_10037292_10066351 9397 . G . . END=9397 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 9398 . A . . END=9399 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9400 . C . . END=9400 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,999 -20_10037292_10066351 9401 . T . . END=9410 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 9411 . A . . END=9411 GT:DP:GQ:MIN_DP:PL 0/0:33:76:33:0,76,993 -20_10037292_10066351 9412 . T . . END=9414 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 9415 . T . . END=9419 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 -20_10037292_10066351 9420 . T . . END=9426 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 9427 . T . . END=9427 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,933 -20_10037292_10066351 9428 . A . . END=9437 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,902 -20_10037292_10066351 9438 . T . . END=9438 GT:DP:GQ:MIN_DP:PL 0/0:31:67:31:0,67,919 -20_10037292_10066351 9439 . T . . END=9439 GT:DP:GQ:MIN_DP:PL 0/0:33:39:33:0,39,897 -20_10037292_10066351 9440 . T . . END=9454 GT:DP:GQ:MIN_DP:PL 0/0:33:81:29:0,81,918 -20_10037292_10066351 9455 . G . . END=9455 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,898 -20_10037292_10066351 9456 . G . . END=9468 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,883 -20_10037292_10066351 9469 . T . . END=9478 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,1125 -20_10037292_10066351 9479 . A . . END=9479 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,801 -20_10037292_10066351 9480 . A . . END=9480 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 9481 . G . . END=9481 GT:DP:GQ:MIN_DP:PL 0/0:26:65:26:0,65,756 -20_10037292_10066351 9482 . C . . END=9484 GT:DP:GQ:MIN_DP:PL 0/0:27:72:24:0,72,748 -20_10037292_10066351 9485 . A . . END=9485 GT:DP:GQ:MIN_DP:PL 0/0:27:44:27:0,44,682 -20_10037292_10066351 9486 . A . . END=9486 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,746 -20_10037292_10066351 9487 . C . . END=9504 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,847 -20_10037292_10066351 9505 . A . . END=9505 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,804 -20_10037292_10066351 9506 . C . . END=9507 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 9508 . T . . END=9508 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,802 -20_10037292_10066351 9509 . G . . END=9511 GT:DP:GQ:MIN_DP:PL 0/0:26:72:24:0,72,758 -20_10037292_10066351 9512 . T . . END=9512 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,684 -20_10037292_10066351 9513 . C . . END=9526 GT:DP:GQ:MIN_DP:PL 0/0:26:60:25:0,60,900 -20_10037292_10066351 9527 . C . . END=9530 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 9531 . C . . END=9534 GT:DP:GQ:MIN_DP:PL 0/0:27:69:23:0,69,651 -20_10037292_10066351 9535 . A . . END=9535 GT:DP:GQ:MIN_DP:PL 0/0:23:57:23:0,57,659 -20_10037292_10066351 9536 . T C, 148.64 . BaseQRankSum=-0.564;DP=21;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=75600,21;ReadPosRankSum=0.860 GT:AD:DP:GQ:PL:SB 0/1:14,7,0:21:99:156,0,353,197,374,571:3,11,5,2 -20_10037292_10066351 9537 . T . . END=9537 GT:DP:GQ:MIN_DP:PL 0/0:23:53:23:0,53,658 -20_10037292_10066351 9538 . C . . END=9538 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 9539 . A . . END=9539 GT:DP:GQ:MIN_DP:PL 0/0:24:22:24:0,22,564 -20_10037292_10066351 9540 . A . . END=9540 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 9541 . C . . END=9541 GT:DP:GQ:MIN_DP:PL 0/0:23:52:23:0,52,683 -20_10037292_10066351 9542 . T . . END=9542 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,683 -20_10037292_10066351 9543 . C . . END=9546 GT:DP:GQ:MIN_DP:PL 0/0:24:69:23:0,69,752 -20_10037292_10066351 9547 . T . . END=9548 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 9549 . A . . END=9549 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,760 -20_10037292_10066351 9550 . A . . END=9555 GT:DP:GQ:MIN_DP:PL 0/0:28:78:27:0,78,1170 -20_10037292_10066351 9556 . T . . END=9556 GT:DP:GQ:MIN_DP:PL 0/0:28:55:28:0,55,776 -20_10037292_10066351 9557 . A . . END=9557 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,778 -20_10037292_10066351 9558 . A . . END=9558 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,765 -20_10037292_10066351 9559 . A . . END=9561 GT:DP:GQ:MIN_DP:PL 0/0:27:70:26:0,70,832 -20_10037292_10066351 9562 . C . . END=9564 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 9565 . G . . END=9565 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 9566 . T . . END=9567 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9568 . A . . END=9569 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 9570 . T . . END=9570 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,890 -20_10037292_10066351 9571 . C . . END=9578 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,983 -20_10037292_10066351 9579 . T . . END=9582 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,985 -20_10037292_10066351 9583 . A . . END=9583 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,921 -20_10037292_10066351 9584 . T . . END=9588 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,935 -20_10037292_10066351 9589 . A . . END=9589 GT:DP:GQ:MIN_DP:PL 0/0:32:77:32:0,77,898 -20_10037292_10066351 9590 . C . . END=9596 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,964 -20_10037292_10066351 9597 . C . . END=9597 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,881 -20_10037292_10066351 9598 . G . . END=9602 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,901 -20_10037292_10066351 9603 . A . . END=9627 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 9628 . A . . END=9628 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9629 . A . . END=9637 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1172 -20_10037292_10066351 9638 . A . . END=9638 GT:DP:GQ:MIN_DP:PL 0/0:36:68:36:0,68,946 -20_10037292_10066351 9639 . A . . END=9641 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9642 . A . . END=9643 GT:DP:GQ:MIN_DP:PL 0/0:34:83:33:0,83,925 -20_10037292_10066351 9644 . T . . END=9648 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1015 -20_10037292_10066351 9649 . T . . END=9649 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,980 -20_10037292_10066351 9650 . C . . END=9652 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1023 -20_10037292_10066351 9653 . T . . END=9653 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1058 -20_10037292_10066351 9654 . T . . END=9655 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1065 -20_10037292_10066351 9656 . T . . END=9657 GT:DP:GQ:MIN_DP:PL 0/0:38:92:37:0,92,1061 -20_10037292_10066351 9658 . T . . END=9658 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1072 -20_10037292_10066351 9659 . T . . END=9659 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1070 -20_10037292_10066351 9660 . A . . END=9660 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9661 . T . . END=9662 GT:DP:GQ:MIN_DP:PL 0/0:38:84:37:0,84,1058 -20_10037292_10066351 9663 . T . . END=9848 GT:DP:GQ:MIN_DP:PL 0/0:45:99:37:0,102,1151 -20_10037292_10066351 9849 . A . . END=9850 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1083 -20_10037292_10066351 9851 . T . . END=9859 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,100,1156 -20_10037292_10066351 12912 . G . . END=12913 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 12914 . G . . END=12915 GT:DP:GQ:MIN_DP:PL 0/0:38:81:37:0,81,1160 -20_10037292_10066351 12916 . A . . END=12921 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 12922 . A . . END=12922 GT:DP:GQ:MIN_DP:PL 0/0:34:76:34:0,76,1008 -20_10037292_10066351 12923 . A . . END=12925 GT:DP:GQ:MIN_DP:PL 0/0:34:96:32:0,96,980 -20_10037292_10066351 12926 . C . . END=12926 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,899 -20_10037292_10066351 12927 . C . . END=12928 GT:DP:GQ:MIN_DP:PL 0/0:32:95:32:0,95,965 -20_10037292_10066351 12929 . G . . END=12929 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1119 -20_10037292_10066351 12930 . A . . END=12930 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 12931 . A . . END=12931 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,999 -20_10037292_10066351 12932 . A . . END=12932 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,994 -20_10037292_10066351 12933 . A . . END=12936 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 12937 . T . . END=12939 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 12940 . A . . END=12940 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 12941 . C . . END=12941 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1007 -20_10037292_10066351 12942 . A . . END=12942 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,1056 -20_10037292_10066351 12943 . A . . END=12943 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1017 -20_10037292_10066351 12944 . A . . END=12946 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 12947 . T . . END=12947 GT:DP:GQ:MIN_DP:PL 0/0:32:55:32:0,55,902 -20_10037292_10066351 12948 . G . . END=12953 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 12954 . A . . END=12956 GT:DP:GQ:MIN_DP:PL 0/0:32:70:29:0,70,876 -20_10037292_10066351 12957 . A . . END=12957 GT:DP:GQ:MIN_DP:PL 0/0:29:58:29:0,58,804 -20_10037292_10066351 12958 . A . . END=12961 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,857 -20_10037292_10066351 12962 . G . . END=12967 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,840 -20_10037292_10066351 12968 . A . . END=12968 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,805 -20_10037292_10066351 12969 . G . . END=12969 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,914 -20_10037292_10066351 12970 . C . . END=12970 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,853 -20_10037292_10066351 12971 . T . . END=12972 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,758 -20_10037292_10066351 12973 . A . . END=12975 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 12976 . A . . END=12978 GT:DP:GQ:MIN_DP:PL 0/0:29:60:28:0,60,821 -20_10037292_10066351 12979 . A . . END=12979 GT:DP:GQ:MIN_DP:PL 0/0:29:57:29:0,57,846 -20_10037292_10066351 12980 . G . . END=12980 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 12981 . G . . END=12990 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,832 -20_10037292_10066351 12991 . A . . END=12993 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 12994 . A . . END=12994 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,884 -20_10037292_10066351 12995 . C . . END=12995 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,828 -20_10037292_10066351 12996 . G . . END=13013 GT:DP:GQ:MIN_DP:PL 0/0:31:81:28:0,81,857 -20_10037292_10066351 13014 . A . . END=13016 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 13017 . C . . END=13018 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13019 . C . . END=13019 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,851 -20_10037292_10066351 13020 . A . . END=13021 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 13022 . G . . END=13023 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 13024 . A . . END=13024 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,845 -20_10037292_10066351 13025 . A . . END=13026 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 13027 . A . . END=13027 GT:DP:GQ:MIN_DP:PL 0/0:26:66:26:0,66,815 -20_10037292_10066351 13028 . G . . END=13028 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 13029 . T . . END=13029 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,733 -20_10037292_10066351 13030 . A . . END=13034 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,845 -20_10037292_10066351 13035 . G . . END=13035 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,837 -20_10037292_10066351 13036 . T . . END=13036 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,788 -20_10037292_10066351 13037 . G . . END=13037 GT:DP:GQ:MIN_DP:PL 0/0:28:67:28:0,67,839 -20_10037292_10066351 13038 . T . . END=13040 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,833 -20_10037292_10066351 13041 . A . . END=13041 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,782 -20_10037292_10066351 13042 . T . . END=13051 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,835 -20_10037292_10066351 13052 . A . . END=13052 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13053 . G . . END=13054 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13055 . T . . END=13055 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,1086 -20_10037292_10066351 13056 . C . . END=13057 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 13058 . A . . END=13058 GT:DP:GQ:MIN_DP:PL 0/0:40:69:40:0,69,1150 -20_10037292_10066351 13059 . T . . END=13059 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,111,1665 -20_10037292_10066351 13060 . T . . END=13060 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1152 -20_10037292_10066351 13061 . G . . END=13061 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 13062 . G . . END=13062 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1169 -20_10037292_10066351 13063 . T . . END=13063 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1125 -20_10037292_10066351 13064 . T . . END=13064 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 13065 . T . . END=13065 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1139 -20_10037292_10066351 13066 . T . . END=13066 GT:DP:GQ:MIN_DP:PL 0/0:38:74:38:0,74,1124 -20_10037292_10066351 13067 . C . . END=13067 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1143 -20_10037292_10066351 13068 . A . . END=13068 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1171 -20_10037292_10066351 13069 . C . . END=13069 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1174 -20_10037292_10066351 13070 . A . . END=13070 GT:DP:GQ:MIN_DP:PL 0/0:41:68:41:0,68,1170 -20_10037292_10066351 13071 . T . . END=13072 GT:DP:GQ:MIN_DP:PL 0/0:40:74:40:0,74,1159 -20_10037292_10066351 13073 . G . . END=13089 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,114,1259 -20_10037292_10066351 13090 . A . . END=13090 GT:DP:GQ:MIN_DP:PL 0/0:45:92:45:0,92,1316 -20_10037292_10066351 13091 . G . . END=13182 GT:DP:GQ:MIN_DP:PL 0/0:49:99:43:0,114,1309 -20_10037292_10066351 13183 . A . . END=13183 GT:DP:GQ:MIN_DP:PL 0/0:46:90:46:0,90,1291 -20_10037292_10066351 13184 . A . . END=13184 GT:DP:GQ:MIN_DP:PL 0/0:46:99:46:0,111,1665 -20_10037292_10066351 13185 . T A, 0 . BaseQRankSum=-0.574;DP=43;ExcessHet=0.0000;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=154800,43;ReadPosRankSum=2.040 GT:AD:DP:GQ:PL:SB 0/0:40,2,0:42:60:0,60,1194,120,1200,1259:20,20,2,0 -20_10037292_10066351 13186 . A . . END=13187 GT:DP:GQ:MIN_DP:PL 0/0:41:82:39:0,82,1220 -20_10037292_10066351 13188 . A . . END=13188 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1137 -20_10037292_10066351 13189 . A . . END=13189 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1126 -20_10037292_10066351 13190 . A . . END=13190 GT:DP:GQ:MIN_DP:PL 0/0:38:79:38:0,79,1147 -20_10037292_10066351 13191 . G . . END=13192 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1118 -20_10037292_10066351 13193 . C . . END=13193 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1575 -20_10037292_10066351 13194 . A . . END=13195 GT:DP:GQ:MIN_DP:PL 0/0:39:83:38:0,83,1147 -20_10037292_10066351 13196 . T . . END=13196 GT:DP:GQ:MIN_DP:PL 0/0:39:67:39:0,67,1070 -20_10037292_10066351 13197 . A . . END=13197 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 13198 . T . . END=13199 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,105,1575 -20_10037292_10066351 13200 . T . . END=13200 GT:DP:GQ:MIN_DP:PL 0/0:42:72:42:0,72,1137 -20_10037292_10066351 13201 . T . . END=13205 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,101,1208 -20_10037292_10066351 13206 . C . . END=13206 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1171 -20_10037292_10066351 13207 . T . . END=13207 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1156 -20_10037292_10066351 13208 . C . . END=13209 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 13210 . A . . END=13210 GT:DP:GQ:MIN_DP:PL 0/0:39:83:39:0,83,1168 -20_10037292_10066351 13211 . G . . END=13211 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 13212 . C . . END=13212 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1103 -20_10037292_10066351 13213 . T . . END=13214 GT:DP:GQ:MIN_DP:PL 0/0:42:90:41:0,90,1196 -20_10037292_10066351 13215 . T . . END=13215 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,110,1229 -20_10037292_10066351 13216 . T . . END=13216 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1208 -20_10037292_10066351 13217 . C . . END=13217 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,111,1665 -20_10037292_10066351 13218 . A . . END=13218 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1276 -20_10037292_10066351 13219 . A . . END=13219 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,111,1665 -20_10037292_10066351 13220 . G . . END=13220 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1192 -20_10037292_10066351 13221 . T . . END=13225 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,1157 -20_10037292_10066351 13226 . A . . END=13227 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 13228 . C . . END=13229 GT:DP:GQ:MIN_DP:PL 0/0:39:92:38:0,92,1150 -20_10037292_10066351 13230 . G . . END=13230 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1177 -20_10037292_10066351 13231 . G . . END=13231 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1185 -20_10037292_10066351 13232 . A . . END=13232 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1172 -20_10037292_10066351 13233 . A . . END=13236 GT:DP:GQ:MIN_DP:PL 0/0:39:82:38:0,82,1118 -20_10037292_10066351 13237 . T . . END=13237 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 13238 . A . . END=13239 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1119 -20_10037292_10066351 13240 . C . . END=13240 GT:DP:GQ:MIN_DP:PL 0/0:38:90:38:0,90,1350 -20_10037292_10066351 13241 . C . . END=13242 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1089 -20_10037292_10066351 13243 . A . . END=13243 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 13244 . A . . END=13244 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1110 -20_10037292_10066351 13245 . G . . END=13245 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1076 -20_10037292_10066351 13246 . G . . END=13246 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1062 -20_10037292_10066351 13247 . A . . END=13249 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 13250 . T . . END=13251 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,1004 -20_10037292_10066351 13252 . A . . END=13252 GT:DP:GQ:MIN_DP:PL 0/0:34:82:34:0,82,1111 -20_10037292_10066351 13253 . G . . END=13254 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,1028 -20_10037292_10066351 13255 . T . . END=13255 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 13256 . T . . END=13256 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,1058 -20_10037292_10066351 13257 . T . . END=13257 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1036 -20_10037292_10066351 13258 . C . . END=13258 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,1048 -20_10037292_10066351 13259 . A . . END=13259 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1082 -20_10037292_10066351 13260 . C . . END=13260 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,1084 -20_10037292_10066351 13261 . A . . END=13262 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13263 . A . . END=13263 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,1018 -20_10037292_10066351 13264 . T . . END=13264 GT:DP:GQ:MIN_DP:PL 0/0:35:77:35:0,77,1107 -20_10037292_10066351 13265 . G . . END=13265 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,1009 -20_10037292_10066351 13266 . T . . END=13268 GT:DP:GQ:MIN_DP:PL 0/0:34:70:34:0,70,1039 -20_10037292_10066351 13269 . G . . END=13269 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13270 . A . . END=13271 GT:DP:GQ:MIN_DP:PL 0/0:34:76:34:0,76,1057 -20_10037292_10066351 13272 . C . . END=13272 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1005 -20_10037292_10066351 13273 . A . . END=13275 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1116 -20_10037292_10066351 13276 . A . . END=13276 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1156 -20_10037292_10066351 13277 . G . . END=13277 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 13278 . A . . END=13278 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1120 -20_10037292_10066351 13279 . C . . END=13279 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1119 -20_10037292_10066351 13280 . A . . END=13280 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1124 -20_10037292_10066351 13281 . T . . END=13281 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 13282 . C . . END=13282 GT:DP:GQ:MIN_DP:PL 0/0:36:58:36:0,58,1060 -20_10037292_10066351 13283 . T . . END=13285 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1129 -20_10037292_10066351 13286 . T . . END=13286 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13287 . A . . END=13292 GT:DP:GQ:MIN_DP:PL 0/0:36:75:35:0,75,1083 -20_10037292_10066351 13293 . T . . END=13293 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1243 -20_10037292_10066351 13294 . G . . END=13294 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1142 -20_10037292_10066351 13295 . T . . END=13295 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13296 . T . . END=13300 GT:DP:GQ:MIN_DP:PL 0/0:37:74:36:0,74,1111 -20_10037292_10066351 13301 . C . . END=13301 GT:DP:GQ:MIN_DP:PL 0/0:35:84:35:0,84,1260 -20_10037292_10066351 13302 . T . . END=13303 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,1126 -20_10037292_10066351 13304 . T . . END=13309 GT:DP:GQ:MIN_DP:PL 0/0:34:65:33:0,65,1022 -20_10037292_10066351 13310 . T . . END=13310 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,1010 -20_10037292_10066351 13311 . C . . END=13311 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,1004 -20_10037292_10066351 13312 . C . . END=13312 GT:DP:GQ:MIN_DP:PL 0/0:30:57:30:0,57,928 -20_10037292_10066351 13313 . T . . END=13314 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 13315 . T . . END=13317 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,960 -20_10037292_10066351 13318 . C . . END=13318 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1053 -20_10037292_10066351 13319 . T . . END=13319 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1003 -20_10037292_10066351 13320 . T . . END=13320 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1013 -20_10037292_10066351 13321 . T . . END=13321 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1100 -20_10037292_10066351 13322 . C . . END=13322 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1089 -20_10037292_10066351 13323 . T . . END=13348 GT:DP:GQ:MIN_DP:PL 0/0:37:99:33:0,99,1043 -20_10037292_10066351 13349 . G . . END=13351 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,1073 -20_10037292_10066351 13352 . T . . END=13358 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1350 -20_10037292_10066351 13359 . T . . END=13359 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1077 -20_10037292_10066351 13360 . A . . END=13374 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,925 -20_10037292_10066351 13375 . C . . END=13377 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 13378 . T . . END=13378 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13379 . G . . END=13382 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1067 -20_10037292_10066351 13383 . T . . END=13383 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1059 -20_10037292_10066351 13384 . G . . END=13385 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13386 . T . . END=13386 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 13387 . C . . END=13387 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1057 -20_10037292_10066351 13388 . T . . END=13395 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 13396 . C . . END=13396 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1006 -20_10037292_10066351 13397 . A . . END=13404 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 13405 . T . . END=13406 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 13407 . T . . END=13408 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13409 . C . . END=13409 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1023 -20_10037292_10066351 13410 . T . . END=13412 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13413 . T . . END=13416 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,1215 -20_10037292_10066351 13417 . T . . END=13417 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,940 -20_10037292_10066351 13418 . A . . END=13425 GT:DP:GQ:MIN_DP:PL 0/0:31:75:29:0,75,1125 -20_10037292_10066351 13426 . G . . END=13426 GT:DP:GQ:MIN_DP:PL 0/0:29:57:29:0,57,831 -20_10037292_10066351 13427 . A . . END=13452 GT:DP:GQ:MIN_DP:PL 0/0:25:62:23:0,62,762 -20_10037292_10066351 13453 . A . . END=13453 GT:DP:GQ:MIN_DP:PL 0/0:24:45:24:0,45,732 -20_10037292_10066351 13454 . T . . END=13455 GT:DP:GQ:MIN_DP:PL 0/0:25:66:25:0,66,990 -20_10037292_10066351 13456 . C . . END=13456 GT:DP:GQ:MIN_DP:PL 0/0:25:52:25:0,52,796 -20_10037292_10066351 13457 . T . . END=13466 GT:DP:GQ:MIN_DP:PL 0/0:24:60:22:0,60,900 -20_10037292_10066351 13467 . T . . END=13472 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,1080 -20_10037292_10066351 13473 . A . . END=13473 GT:DP:GQ:MIN_DP:PL 0/0:25:64:25:0,64,737 -20_10037292_10066351 13474 . A . . END=13478 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,849 -20_10037292_10066351 13479 . G . . END=13479 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,808 -20_10037292_10066351 13480 . G . . END=13489 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 13490 . A . . END=13492 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,845 -20_10037292_10066351 13493 . A . . END=13493 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 13494 . G . . END=13496 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 13497 . A . . END=13508 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 13509 . C . . END=13510 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,875 -20_10037292_10066351 13511 . C . . END=13513 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 13514 . A . . END=13517 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 13518 . T . . END=13518 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,931 -20_10037292_10066351 13519 . T . . END=13519 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 13520 . T . . END=13528 GT:DP:GQ:MIN_DP:PL 0/0:28:78:27:0,78,1170 -20_10037292_10066351 13529 . C . . END=13529 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,847 -20_10037292_10066351 13530 . T . . END=13534 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,862 -20_10037292_10066351 13535 . T . . END=13537 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 13538 . G . . END=13538 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,931 -20_10037292_10066351 13539 . G . . END=13539 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,893 -20_10037292_10066351 13540 . A . . END=13542 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,890 -20_10037292_10066351 13543 . C . . END=13543 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,891 -20_10037292_10066351 13544 . A . . END=13544 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,870 -20_10037292_10066351 13545 . C . . END=13545 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,818 -20_10037292_10066351 13546 . G . . END=13547 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,840 -20_10037292_10066351 13548 . T . . END=13548 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13549 . A . . END=13554 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 13555 . A . . END=13555 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13556 . T . . END=13556 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,969 -20_10037292_10066351 13557 . A . . END=13557 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1019 -20_10037292_10066351 13558 . C . . END=13558 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,940 -20_10037292_10066351 13559 . T . . END=13559 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1012 -20_10037292_10066351 13560 . C . . END=13560 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1034 -20_10037292_10066351 13561 . T . . END=13564 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,939 -20_10037292_10066351 13565 . C . . END=13565 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,961 -20_10037292_10066351 13566 . C . . END=13595 GT:DP:GQ:MIN_DP:PL 0/0:37:99:33:0,99,1037 -20_10037292_10066351 13596 . T . . END=13596 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1054 -20_10037292_10066351 13597 . G . . END=13606 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 13607 . G . . END=13626 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,1003 -20_10037292_10066351 13627 . A . . END=13627 GT:DP:GQ:MIN_DP:PL 0/0:32:85:32:0,85,973 -20_10037292_10066351 13628 . A . . END=13629 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 13630 . T . . END=13630 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,886 -20_10037292_10066351 13631 . G . . END=13631 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13632 . A . . END=13633 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13634 . G . . END=13634 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13635 . T . . END=13635 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,888 -20_10037292_10066351 13636 . T . . END=13636 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13637 . T . . END=13637 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13638 . G . . END=13641 GT:DP:GQ:MIN_DP:PL 0/0:33:86:31:0,86,974 -20_10037292_10066351 13642 . T . . END=13643 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13644 . T . . END=13644 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 13645 . C . . END=13645 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13646 . C . . END=13648 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 13649 . G . . END=13649 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13650 . C . . END=13651 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13652 . G . . END=13654 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13655 . G . . END=13661 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 13662 . A . . END=13666 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,924 -20_10037292_10066351 13667 . A . . END=13667 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,879 -20_10037292_10066351 13668 . A . . END=13668 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,984 -20_10037292_10066351 13669 . G . . END=13669 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,931 -20_10037292_10066351 13670 . T . . END=13674 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,999 -20_10037292_10066351 13675 . G . . END=13675 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1018 -20_10037292_10066351 13676 . G . . END=13692 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1081 -20_10037292_10066351 13693 . C . . END=13696 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13697 . T . . END=13697 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1068 -20_10037292_10066351 13698 . C . . END=13698 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 13699 . T . . END=13699 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1117 -20_10037292_10066351 13700 . G . . END=13706 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,945 -20_10037292_10066351 13707 . G . . END=13708 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,1046 -20_10037292_10066351 13709 . C . . END=13715 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,108,1620 -20_10037292_10066351 13716 . T . . END=13716 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1230 -20_10037292_10066351 13717 . C . . END=13719 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,105,1575 -20_10037292_10066351 13720 . C . . END=13721 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1111 -20_10037292_10066351 13722 . T . . END=13724 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1174 -20_10037292_10066351 13725 . G . . END=13726 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1107 -20_10037292_10066351 13727 . A . . END=13728 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 13729 . T . . END=13729 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,981 -20_10037292_10066351 13730 . A . . END=13735 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1056 -20_10037292_10066351 13736 . T . . END=13736 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,862 -20_10037292_10066351 13737 . A . . END=13737 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 13738 . G . . END=13738 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1134 -20_10037292_10066351 13739 . G . . END=13740 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 13741 . T . . END=13741 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1018 -20_10037292_10066351 13742 . G . . END=13745 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 13746 . A . . END=13749 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 13750 . G . . END=13750 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,960 -20_10037292_10066351 13751 . C . . END=13756 GT:DP:GQ:MIN_DP:PL 0/0:34:93:32:0,93,964 -20_10037292_10066351 13757 . A . . END=13757 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,875 -20_10037292_10066351 13758 . A . . END=13758 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,973 -20_10037292_10066351 13759 . T . . END=13759 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,900 -20_10037292_10066351 13760 . G . . END=13761 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13762 . A . . END=13762 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,932 -20_10037292_10066351 13763 . C . . END=13763 GT:DP:GQ:MIN_DP:PL 0/0:33:53:33:0,53,879 -20_10037292_10066351 13764 . A . . END=13764 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13765 . T . . END=13765 GT:DP:GQ:MIN_DP:PL 0/0:33:30:33:0,30,748 -20_10037292_10066351 13766 . G . . END=13769 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13770 . G . . END=13770 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,975 -20_10037292_10066351 13771 . G . . END=13771 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13772 . T . . END=13773 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,924 -20_10037292_10066351 13774 . A . . END=13774 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,959 -20_10037292_10066351 13775 . T . . END=13775 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,970 -20_10037292_10066351 13776 . A . . END=13776 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,893 -20_10037292_10066351 13777 . A . . END=13777 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,923 -20_10037292_10066351 13778 . G . . END=13778 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,997 -20_10037292_10066351 13779 . C . . END=13788 GT:DP:GQ:MIN_DP:PL 0/0:33:91:32:0,91,956 -20_10037292_10066351 13789 . T . . END=13789 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13790 . T . . END=13800 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,962 -20_10037292_10066351 13801 . A . . END=13801 GT:DP:GQ:MIN_DP:PL 0/0:34:72:34:0,72,920 -20_10037292_10066351 13802 . C . . END=13802 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13803 . C . . END=13803 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,973 -20_10037292_10066351 13804 . A . . END=13804 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13805 . G . . END=13806 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13807 . C . . END=13807 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,908 -20_10037292_10066351 13808 . T . . END=13808 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13809 . C . . END=13809 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,903 -20_10037292_10066351 13810 . A . . END=13810 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13811 . C . . END=13811 GT:DP:GQ:MIN_DP:PL 0/0:31:71:31:0,71,847 -20_10037292_10066351 13812 . T . . END=13814 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 13815 . C . . END=13815 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,877 -20_10037292_10066351 13816 . A . . END=13819 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13820 . T . . END=13820 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,877 -20_10037292_10066351 13821 . T . . END=13821 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13822 . A . . END=13822 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 13823 . C . . END=13823 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 13824 . T . . END=13825 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,852 -20_10037292_10066351 13826 . C . . END=13830 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,881 -20_10037292_10066351 13831 . G . . END=13831 GT:DP:GQ:MIN_DP:PL 0/0:32:61:32:0,61,867 -20_10037292_10066351 13832 . T . . END=13832 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,806 -20_10037292_10066351 13833 . T . . END=13834 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13835 . G . . END=13836 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 13837 . G . . END=13837 GT:DP:GQ:MIN_DP:PL 0/0:32:71:32:0,71,944 -20_10037292_10066351 13838 . A . . END=13845 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,959 -20_10037292_10066351 13846 . T . . END=13846 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,884 -20_10037292_10066351 13847 . T . . END=13847 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13848 . G . . END=13853 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,987 -20_10037292_10066351 13854 . A . . END=13857 GT:DP:GQ:MIN_DP:PL 0/0:33:78:32:0,78,1170 -20_10037292_10066351 13858 . A . . END=13858 GT:DP:GQ:MIN_DP:PL 0/0:35:84:35:0,84,1260 -20_10037292_10066351 13859 . T . . END=13859 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 13860 . T . . END=13860 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,994 -20_10037292_10066351 13861 . C . . END=13863 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 13864 . A . . END=13864 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,978 -20_10037292_10066351 13865 . C . . END=13867 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13868 . T . . END=13868 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,998 -20_10037292_10066351 13869 . G . . END=13874 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,925 -20_10037292_10066351 13875 . A . . END=13875 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,910 -20_10037292_10066351 13876 . A . . END=13880 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13881 . A . . END=13881 GT:DP:GQ:MIN_DP:PL 0/0:29:68:29:0,68,849 -20_10037292_10066351 13882 . C . . END=13883 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13884 . T . . END=13885 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13886 . A . . END=13886 GT:DP:GQ:MIN_DP:PL 0/0:32:73:32:0,73,975 -20_10037292_10066351 13887 . G . . END=13892 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,896 -20_10037292_10066351 13893 . G . . END=13893 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,973 -20_10037292_10066351 13894 . T . . END=13895 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13896 . A . . END=13896 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,960 -20_10037292_10066351 13897 . T . . END=13897 GT:DP:GQ:MIN_DP:PL 0/0:32:70:32:0,70,922 -20_10037292_10066351 13898 . T . . END=13898 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,971 -20_10037292_10066351 13899 . T . . END=13900 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 13901 . T . . END=13901 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,978 -20_10037292_10066351 13902 . A . . END=13902 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,924 -20_10037292_10066351 13903 . A . . END=13903 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13904 . A . . END=13905 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 13906 . A . . END=13906 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13907 . A . . END=13907 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,932 -20_10037292_10066351 13908 . A . . END=13909 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13910 . G . . END=13912 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,950 -20_10037292_10066351 13913 . G . . END=13914 GT:DP:GQ:MIN_DP:PL 0/0:31:76:30:0,76,876 -20_10037292_10066351 13915 . T . . END=13915 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,967 -20_10037292_10066351 13916 . T . . END=13920 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 13921 . G . . END=13921 GT:DP:GQ:MIN_DP:PL 0/0:32:46:32:0,46,838 -20_10037292_10066351 13922 . G . . END=13922 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,895 -20_10037292_10066351 13923 . C . . END=13923 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13924 . T . . END=13924 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1032 -20_10037292_10066351 13925 . C . . END=13925 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 13926 . A . . END=13926 GT:DP:GQ:MIN_DP:PL 0/0:34:57:34:0,57,966 -20_10037292_10066351 13927 . C . . END=13927 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,104,1029 -20_10037292_10066351 13928 . A . . END=13928 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1038 -20_10037292_10066351 13929 . G . . END=13929 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1017 -20_10037292_10066351 13930 . T . . END=13931 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 13932 . C . . END=13933 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1045 -20_10037292_10066351 13934 . G . . END=13934 GT:DP:GQ:MIN_DP:PL 0/0:35:83:35:0,83,1030 -20_10037292_10066351 13935 . C . . END=13936 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1052 -20_10037292_10066351 13937 . G . . END=13937 GT:DP:GQ:MIN_DP:PL 0/0:35:77:35:0,77,1064 -20_10037292_10066351 13938 . G . . END=13938 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,991 -20_10037292_10066351 13939 . C . . END=13939 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13940 . T . . END=13941 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 13942 . T . . END=13943 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 13944 . C . . END=13944 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1007 -20_10037292_10066351 13945 . A . . END=13946 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13947 . G . . END=13953 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1156 -20_10037292_10066351 13954 . A . . END=13954 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1054 -20_10037292_10066351 13955 . G . . END=13958 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,102,1530 -20_10037292_10066351 13959 . C . . END=13959 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1165 -20_10037292_10066351 13960 . T . . END=13965 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1101 -20_10037292_10066351 13966 . C . . END=13966 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1180 -20_10037292_10066351 13967 . T . . END=13967 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1064 -20_10037292_10066351 13968 . C . . END=13969 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,111,1155 -20_10037292_10066351 13970 . G . . END=13970 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1159 -20_10037292_10066351 13971 . G . . END=13971 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1061 -20_10037292_10066351 13972 . G . . END=13972 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1094 -20_10037292_10066351 13973 . G . . END=13975 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 13976 . A . . END=13976 GT:DP:GQ:MIN_DP:PL 0/0:39:93:39:0,93,1112 -20_10037292_10066351 13977 . C . . END=13979 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,108,1620 -20_10037292_10066351 13980 . C . . END=13980 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1102 -20_10037292_10066351 13981 . A . . END=13985 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1530 -20_10037292_10066351 13986 . G . . END=13987 GT:DP:GQ:MIN_DP:PL 0/0:37:94:36:0,94,1097 -20_10037292_10066351 13988 . T . . END=13988 GT:DP:GQ:MIN_DP:PL 0/0:37:88:37:0,88,1106 -20_10037292_10066351 13989 . T . . END=13995 GT:DP:GQ:MIN_DP:PL 0/0:35:92:34:0,92,1082 -20_10037292_10066351 13996 . A . . END=13999 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,102,1029 -20_10037292_10066351 14000 . C . . END=14004 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 14005 . G . . END=14005 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 14006 . G . . END=14006 GT:DP:GQ:MIN_DP:PL 0/0:38:70:38:0,70,1092 -20_10037292_10066351 14007 . C . . END=14007 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1050 -20_10037292_10066351 14008 . A . . END=14010 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 14011 . G . . END=14011 GT:DP:GQ:MIN_DP:PL 0/0:33:65:33:0,65,969 -20_10037292_10066351 14012 . G . . END=14012 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1016 -20_10037292_10066351 14013 . G . . END=14014 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,962 -20_10037292_10066351 14015 . C . . END=14015 GT:DP:GQ:MIN_DP:PL 0/0:35:61:35:0,61,980 -20_10037292_10066351 14016 . A . . END=14016 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1160 -20_10037292_10066351 14017 . G . . END=14017 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1129 -20_10037292_10066351 14018 . C . . END=14018 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,104,884 -20_10037292_10066351 14019 . G . . END=14019 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1038 -20_10037292_10066351 14020 . A . . END=14020 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,114,1158 -20_10037292_10066351 14021 . G . . END=14022 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1108 -20_10037292_10066351 14023 . C . . END=14026 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1138 -20_10037292_10066351 14027 . T . . END=14027 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1053 -20_10037292_10066351 14028 . C . . END=14030 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,101,1155 -20_10037292_10066351 14031 . G . . END=14031 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1034 -20_10037292_10066351 14032 . G . . END=14042 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,102,1197 -20_10037292_10066351 14043 . A . . END=14043 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1196 -20_10037292_10066351 14044 . A . . END=14044 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,117,1755 -20_10037292_10066351 14045 . G . . END=14045 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1338 -20_10037292_10066351 14046 . A . . END=14047 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,117,1755 -20_10037292_10066351 14048 . G . . END=14048 GT:DP:GQ:MIN_DP:PL 0/0:41:98:41:0,98,1245 -20_10037292_10066351 14049 . A . . END=14049 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,117,1755 -20_10037292_10066351 14050 . G . . END=14050 GT:DP:GQ:MIN_DP:PL 0/0:39:74:39:0,74,1093 -20_10037292_10066351 14051 . A . . END=14051 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1234 -20_10037292_10066351 14052 . G . . END=14052 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1192 -20_10037292_10066351 14053 . A . . END=14060 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,107,1225 -20_10037292_10066351 14061 . G . . END=14062 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1200 -20_10037292_10066351 14063 . G . . END=14066 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,102,1263 -20_10037292_10066351 14067 . C . . END=14067 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1199 -20_10037292_10066351 14068 . C . . END=14172 GT:DP:GQ:MIN_DP:PL 0/0:45:99:38:0,99,1117 -20_10037292_10066351 14173 . T . . END=14173 GT:DP:GQ:MIN_DP:PL 0/0:45:78:45:0,78,1309 -20_10037292_10066351 14174 . C . . END=14190 GT:DP:GQ:MIN_DP:PL 0/0:45:99:38:0,108,1227 -20_10037292_10066351 14191 . C . . END=14191 GT:DP:GQ:MIN_DP:PL 0/0:38:65:38:0,65,1134 -20_10037292_10066351 14192 . T . . END=14198 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1137 -20_10037292_10066351 14199 . A . . END=14199 GT:DP:GQ:MIN_DP:PL 0/0:39:72:39:0,72,1156 -20_10037292_10066351 14200 . C . . END=14212 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1266 -20_10037292_10066351 14213 . G . . END=14213 GT:DP:GQ:MIN_DP:PL 0/0:37:91:37:0,91,1138 -20_10037292_10066351 14214 . T . . END=14214 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1093 -20_10037292_10066351 14215 . G . . END=14216 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 14217 . T . . END=14221 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 14222 . G . . END=14228 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1069 -20_10037292_10066351 14229 . C . . END=14229 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1031 -20_10037292_10066351 14230 . A . . END=14238 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1036 -20_10037292_10066351 14239 . T . . END=14239 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1067 -20_10037292_10066351 14240 . T . . END=14243 GT:DP:GQ:MIN_DP:PL 0/0:36:99:33:0,99,1029 -20_10037292_10066351 14244 . A . . END=14244 GT:DP:GQ:MIN_DP:PL 0/0:35:79:35:0,79,1043 -20_10037292_10066351 14245 . T . . END=14246 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1038 -20_10037292_10066351 14247 . A . . END=14249 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1052 -20_10037292_10066351 14250 . T . . END=14250 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,995 -20_10037292_10066351 14251 . T . . END=14253 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 14254 . G . . END=14254 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 14255 . G . . END=14259 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1015 -20_10037292_10066351 14260 . G . . END=14260 GT:DP:GQ:MIN_DP:PL 0/0:32:61:32:0,61,918 -20_10037292_10066351 14261 . A . . END=14261 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1170 -20_10037292_10066351 14262 . C . . END=14266 GT:DP:GQ:MIN_DP:PL 0/0:32:81:29:0,81,1215 -20_10037292_10066351 14267 . A . . END=14268 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,882 -20_10037292_10066351 14269 . C . . END=14269 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,828 -20_10037292_10066351 14270 . C . . END=14273 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 14274 . C . . END=14274 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 14275 . C . . END=14277 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,1080 -20_10037292_10066351 14278 . A . . END=14282 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 14283 . A . . END=14283 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,834 -20_10037292_10066351 14284 . A . . END=14286 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,900 -20_10037292_10066351 14287 . T . . END=14288 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 14289 . A . . END=14289 GT:DP:GQ:MIN_DP:PL 0/0:27:55:27:0,55,782 -20_10037292_10066351 14290 . T . . END=14291 GT:DP:GQ:MIN_DP:PL 0/0:29:72:26:0,72,945 -20_10037292_10066351 14292 . G . . END=14294 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 14295 . T . . END=14295 GT:DP:GQ:MIN_DP:PL 0/0:31:35:31:0,35,906 -20_10037292_10066351 14296 . A . . END=14303 GT:DP:GQ:MIN_DP:PL 0/0:32:74:30:0,74,999 -20_10037292_10066351 14304 . C . . END=14309 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,909 -20_10037292_10066351 14310 . A . . END=14310 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,859 -20_10037292_10066351 14311 . A . . END=14319 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,942 -20_10037292_10066351 14320 . C . . END=14321 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,954 -20_10037292_10066351 14322 . A . . END=14326 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 14327 . G . . END=14327 GT:DP:GQ:MIN_DP:PL 0/0:31:32:31:0,32,833 -20_10037292_10066351 14328 . C . . END=14328 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 14329 . A . . END=14329 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,1013 -20_10037292_10066351 14330 . C . . END=14333 GT:DP:GQ:MIN_DP:PL 0/0:34:93:32:0,93,1033 -20_10037292_10066351 14334 . A . . END=14334 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,955 -20_10037292_10066351 14335 . T . . END=14335 GT:DP:GQ:MIN_DP:PL 0/0:33:77:33:0,77,965 -20_10037292_10066351 14336 . G . . END=14339 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1019 -20_10037292_10066351 14340 . T . . END=14340 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,976 -20_10037292_10066351 14341 . A . . END=14350 GT:DP:GQ:MIN_DP:PL 0/0:40:99:34:0,102,1084 -20_10037292_10066351 14351 . G . . END=14351 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1166 -20_10037292_10066351 14352 . G . . END=14352 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,120,1202 -20_10037292_10066351 14353 . T . . END=14353 GT:DP:GQ:MIN_DP:PL 0/0:40:67:40:0,67,1126 -20_10037292_10066351 14354 . T . . END=14363 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,114,1710 -20_10037292_10066351 14364 . C . . END=14364 GT:DP:GQ:MIN_DP:PL 0/0:41:46:41:0,46,1080 -20_10037292_10066351 14365 . A . . END=14370 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,111,1665 -20_10037292_10066351 14371 . G . . END=14371 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1319 -20_10037292_10066351 14372 . C . . END=14372 GT:DP:GQ:MIN_DP:PL 0/0:44:65:44:0,65,1169 -20_10037292_10066351 14373 . A . . END=14373 GT:DP:GQ:MIN_DP:PL 0/0:42:49:42:0,49,1182 -20_10037292_10066351 14374 . T . . END=14445 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,99,1113 -20_10037292_10066351 14446 . C . . END=14452 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 14453 . C . . END=14455 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 14456 . T . . END=14457 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14458 . A . . END=14466 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 14467 . T . . END=14467 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 14468 . A . . END=14468 GT:DP:GQ:MIN_DP:PL 0/0:34:47:34:0,47,924 -20_10037292_10066351 14469 . C . . END=14473 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14474 . A . . END=14480 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1485 -20_10037292_10066351 14481 . A . . END=14481 GT:DP:GQ:MIN_DP:PL 0/0:38:78:38:0,78,1121 -20_10037292_10066351 14482 . T . . END=14483 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 14484 . A . . END=14485 GT:DP:GQ:MIN_DP:PL 0/0:40:93:39:0,93,1395 -20_10037292_10066351 14486 . A . . END=14486 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,105,1575 -20_10037292_10066351 14487 . C . . END=14487 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1206 -20_10037292_10066351 14488 . A . . END=14488 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1620 -20_10037292_10066351 14489 . T . . END=14489 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1263 -20_10037292_10066351 14490 . G . . END=14499 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,100,1154 -20_10037292_10066351 14500 . G . . END=14501 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1171 -20_10037292_10066351 14502 . C . . END=14505 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 14506 . C . . END=14506 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1092 -20_10037292_10066351 14507 . G . . END=14511 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1217 -20_10037292_10066351 14512 . T . . END=14512 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1193 -20_10037292_10066351 14513 . A . . END=14515 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 14516 . T . . END=14516 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1234 -20_10037292_10066351 14517 . C . . END=14522 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,108,1620 -20_10037292_10066351 14523 . T . . END=14523 GT:DP:GQ:MIN_DP:PL 0/0:41:44:41:0,44,1133 -20_10037292_10066351 14524 . T . . END=14524 GT:DP:GQ:MIN_DP:PL 0/0:41:88:41:0,88,1204 -20_10037292_10066351 14525 . T . . END=14527 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,114,1354 -20_10037292_10066351 14528 . T . . END=14528 GT:DP:GQ:MIN_DP:PL 0/0:42:80:42:0,80,1203 -20_10037292_10066351 14529 . T . . END=14539 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,99,1258 -20_10037292_10066351 14540 . G . . END=14540 GT:DP:GQ:MIN_DP:PL 0/0:43:62:43:0,62,1280 -20_10037292_10066351 14541 . G . . END=14541 GT:DP:GQ:MIN_DP:PL 0/0:44:89:44:0,89,1287 -20_10037292_10066351 14542 . T . . END=14556 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,100,1290 -20_10037292_10066351 14557 . T . . END=14557 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1329 -20_10037292_10066351 14558 . C . . END=14560 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,115,1319 -20_10037292_10066351 14561 . A . . END=14562 GT:DP:GQ:MIN_DP:PL 0/0:44:90:43:0,90,1314 -20_10037292_10066351 14563 . A . . END=14569 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,115,1304 -20_10037292_10066351 14570 . C . . END=14570 GT:DP:GQ:MIN_DP:PL 0/0:43:79:43:0,79,1226 -20_10037292_10066351 14571 . A . . END=14595 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,102,1217 -20_10037292_10066351 14596 . C . . END=14596 GT:DP:GQ:MIN_DP:PL 0/0:40:50:40:0,50,1165 -20_10037292_10066351 14597 . A . . END=14603 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,103,1231 -20_10037292_10066351 14604 . C . . END=14604 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1249 -20_10037292_10066351 14605 . T . . END=14609 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1250 -20_10037292_10066351 14610 . A . . END=14610 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1166 -20_10037292_10066351 14611 . C . . END=14611 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1128 -20_10037292_10066351 14612 . A . . END=14612 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 14613 . T . . END=14615 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1133 -20_10037292_10066351 14616 . C . . END=14616 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1152 -20_10037292_10066351 14617 . T . . END=14619 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1134 -20_10037292_10066351 14620 . T . . END=14620 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1075 -20_10037292_10066351 14621 . C . . END=14622 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1111 -20_10037292_10066351 14623 . C . . END=14623 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1154 -20_10037292_10066351 14624 . C . . END=14624 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 14625 . T . . END=14636 GT:DP:GQ:MIN_DP:PL 0/0:34:81:31:0,81,1132 -20_10037292_10066351 14637 . A . . END=14638 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 14639 . T . . END=14644 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 14645 . G . . END=14655 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,825 -20_10037292_10066351 14656 . C . . END=14665 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,945 -20_10037292_10066351 14666 . A . . END=14666 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,659 -20_10037292_10066351 14667 . T . . END=14668 GT:DP:GQ:MIN_DP:PL 0/0:24:66:23:0,66,990 -20_10037292_10066351 14669 . T . . END=14672 GT:DP:GQ:MIN_DP:PL 0/0:23:57:21:0,57,702 -20_10037292_10066351 14673 . T . . END=14673 GT:DP:GQ:MIN_DP:PL 0/0:23:43:23:0,43,645 -20_10037292_10066351 14674 . G . . END=14692 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,776 -20_10037292_10066351 14693 . T . . END=14697 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,718 -20_10037292_10066351 14698 . A . . END=14698 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,913 -20_10037292_10066351 14699 . T . . END=14699 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,850 -20_10037292_10066351 14700 . A . . END=14703 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,927 -20_10037292_10066351 14704 . A . . END=14704 GT:DP:GQ:MIN_DP:PL 0/0:31:66:31:0,66,939 -20_10037292_10066351 14705 . A . . END=14712 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,954 -20_10037292_10066351 14713 . T . . END=14713 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,944 -20_10037292_10066351 14714 . T . . END=14714 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 14715 . A . . END=14715 GT:DP:GQ:MIN_DP:PL 0/0:31:73:31:0,73,932 -20_10037292_10066351 14716 . C . . END=14722 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 14723 . T . . END=14723 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,948 -20_10037292_10066351 14724 . T . . END=14726 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 14727 . T . . END=14727 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,941 -20_10037292_10066351 14728 . T . . END=14730 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 14731 . A . . END=14731 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 14732 . G . . END=14734 GT:DP:GQ:MIN_DP:PL 0/0:31:82:30:0,82,942 -20_10037292_10066351 14735 . G . . END=14735 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,893 -20_10037292_10066351 14736 . C . . END=14736 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 14737 . A . . END=14737 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf.idx b/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf.idx deleted file mode 100644 index 51256de7d..000000000 Binary files a/hello-nextflow/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf.idx and /dev/null differ diff --git a/hello-nextflow/hello-nf-test/modules/local/samtools/index/main.nf b/hello-nextflow/hello-nf-test/modules/local/samtools/index/main.nf deleted file mode 100644 index 103a47631..000000000 --- a/hello-nextflow/hello-nf-test/modules/local/samtools/index/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - conda "bioconda::samtools=1.20" - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} diff --git a/hello-nextflow/hello-nf-test/nextflow.config b/hello-nextflow/hello-nf-test/nextflow.config deleted file mode 100644 index 86142d64b..000000000 --- a/hello-nextflow/hello-nf-test/nextflow.config +++ /dev/null @@ -1,70 +0,0 @@ -docker.fixOwnership = true - -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = null - - // Output directory - params.outdir = "results_genomics" - - // Accessory files - reference = null - reference_index = null - reference_dict = null - intervals = null - - // Base name for final output file - cohort_name = "my_cohort" -} - -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - my_laptop { - process.executor = 'local' - docker.enabled = true - } - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - process.resourceLimits = [ - memory: 750.GB, - cpus: 200, - time: 30.d - ] - } - demo { - // Primary input (file of input files, one per line) - params.reads_bam = "data/sample_bams.txt" - - // Output directory - params.outdir = "results_genomics" - - // Accessory files - params.reference = "data/ref/ref.fasta" - params.reference_index = "data/ref/ref.fasta.fai" - params.reference_dict = "data/ref/ref.dict" - params.intervals = "data/ref/intervals.bed" - - // Base name for final output file - params.cohort_name = "family_trio" - } -} - -process { - // defaults for all processes - cpus = 2 - memory = 2.GB - // allocations for a specific process - withName: 'GATK_JOINTGENOTYPING' { - cpus = 4 - } -} diff --git a/hello-nextflow/hello-workflow.nf b/hello-nextflow/hello-workflow.nf new file mode 100644 index 000000000..0f54be80c --- /dev/null +++ b/hello-nextflow/hello-workflow.nf @@ -0,0 +1,36 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) +} diff --git a/hello-nextflow/hello-world.nf b/hello-nextflow/hello-world.nf index 53ee46f85..4f672da2b 100644 --- a/hello-nextflow/hello-world.nf +++ b/hello-nextflow/hello-world.nf @@ -1,16 +1,16 @@ #!/usr/bin/env nextflow /* - * Use echo to print 'Hello World!' to standard out + * Use echo to print 'Hello World!' to a file */ process sayHello { output: - stdout + path 'output.txt' script: """ - echo 'Hello World!' + echo 'Hello World!' > output.txt """ } diff --git a/hello-nextflow/nextflow.config b/hello-nextflow/nextflow.config index 187d8f216..0a5fd46b9 100644 --- a/hello-nextflow/nextflow.config +++ b/hello-nextflow/nextflow.config @@ -1,2 +1 @@ -docker.fixOwnership = true -docker.enabled = true +docker.enabled = false diff --git a/hello-nextflow/solutions/hello-world/hello-world-3.nf b/hello-nextflow/solutions/1-hello-world/hello-world-3.nf similarity index 82% rename from hello-nextflow/solutions/hello-world/hello-world-3.nf rename to hello-nextflow/solutions/1-hello-world/hello-world-3.nf index 026a593a8..f2e4b3344 100644 --- a/hello-nextflow/solutions/hello-world/hello-world-3.nf +++ b/hello-nextflow/solutions/1-hello-world/hello-world-3.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow /* - * Use echo to print 'Hello World!' to standard out + * Use echo to print 'Hello World!' to a file */ process sayHello { diff --git a/hello-nextflow/solutions/1-hello-world/hello-world-4.nf b/hello-nextflow/solutions/1-hello-world/hello-world-4.nf new file mode 100644 index 000000000..6236eea21 --- /dev/null +++ b/hello-nextflow/solutions/1-hello-world/hello-world-4.nf @@ -0,0 +1,31 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path 'output.txt' + + script: + """ + echo '$greeting' > output.txt + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'Holà mundo!' + +workflow { + + // emit a greeting + sayHello(params.greeting) +} diff --git a/hello-nextflow/solutions/2-hello-channels/greetings-4.csv b/hello-nextflow/solutions/2-hello-channels/greetings-4.csv new file mode 100644 index 000000000..ce7e03e2a --- /dev/null +++ b/hello-nextflow/solutions/2-hello-channels/greetings-4.csv @@ -0,0 +1,3 @@ +Hello,English +Bonjour,French +Holà,Spanish diff --git a/hello-nextflow/solutions/hello-world/hello-world-5.nf b/hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf similarity index 62% rename from hello-nextflow/solutions/hello-world/hello-world-5.nf rename to hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf index 7d7720960..6190b616a 100644 --- a/hello-nextflow/solutions/hello-world/hello-world-5.nf +++ b/hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow /* - * Use echo to print 'Hello World!' to standard out + * Use echo to print 'Hello World!' to a file */ process sayHello { @@ -11,7 +11,7 @@ process sayHello { val greeting output: - path "output.txt" + path 'output.txt' script: """ @@ -19,10 +19,15 @@ process sayHello { """ } +/* + * Pipeline parameters + */ +params.greeting = 'Holà mundo!' + workflow { // create a channel for inputs - greeting_ch = Channel.of('Hello world!') + greeting_ch = Channel.of('Hello Channels!') // emit a greeting sayHello(greeting_ch) diff --git a/hello-nextflow/solutions/hello-world/hello-world-6.nf b/hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf similarity index 57% rename from hello-nextflow/solutions/hello-world/hello-world-6.nf rename to hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf index 42350793a..5e7a2d50f 100644 --- a/hello-nextflow/solutions/hello-world/hello-world-6.nf +++ b/hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf @@ -1,12 +1,7 @@ #!/usr/bin/env nextflow /* - * Pipeline parameters - */ -params.greeting = "Bonjour le monde!" - -/* - * Use echo to print 'Hello World!' to standard out + * Use echo to print 'Hello World!' to a file */ process sayHello { @@ -16,18 +11,23 @@ process sayHello { val greeting output: - path "output.txt" + path "${greeting}-output.txt" script: """ - echo '$greeting' > "output.txt" + echo '$greeting' > '$greeting-output.txt' """ } +/* + * Pipeline parameters + */ +params.greeting = 'Holà mundo!' + workflow { // create a channel for inputs - greeting_ch = Channel.of(params.greeting) + greeting_ch = Channel.of('Hello','Bonjour','Holà') // emit a greeting sayHello(greeting_ch) diff --git a/hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf b/hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf new file mode 100644 index 000000000..49de2cb65 --- /dev/null +++ b/hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf @@ -0,0 +1,39 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'Holà mundo' + +workflow { + + greetings_array = ['Hello','Bonjour','Holà'] + + // create a channel for inputs + greeting_ch = Channel.of(greetings_array) + .view { "Before flatten: $it" } + .flatten() + .view { "After flatten: $it" } + + // emit a greeting + sayHello(greeting_ch) +} diff --git a/hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf b/hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf new file mode 100644 index 000000000..449366b81 --- /dev/null +++ b/hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf @@ -0,0 +1,41 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' + +workflow { + + greetings_array = ['Hello','Bonjour','Holà'] + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .view { "Before splitCsv: $it" } + .splitCsv() + .view { "After splitCsv: $it" } + .map { line -> line[0] } + .view { "After map: $it" } + + // emit a greeting + sayHello(greeting_ch) +} diff --git a/hello-nextflow/solutions/hello-world/hello-world-9.nf b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf similarity index 65% rename from hello-nextflow/solutions/hello-world/hello-world-9.nf rename to hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf index 22bcb5f07..9516d600f 100644 --- a/hello-nextflow/solutions/hello-world/hello-world-9.nf +++ b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf @@ -1,12 +1,7 @@ #!/usr/bin/env nextflow /* - * Pipeline parameters - */ -params.input_file = "data/greetings.csv" - -/* - * Use echo to print 'Hello World!' to standard out + * Use echo to print 'Hello World!' to a file */ process sayHello { @@ -25,7 +20,7 @@ process sayHello { } /* - * Use a text replace utility to convert the greeting to uppercase + * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { @@ -39,14 +34,21 @@ process convertToUpper { script: """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file} + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' """ } +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' + workflow { // create a channel for inputs from a CSV file - greeting_ch = Channel.fromPath(params.input_file).splitCsv().flatten() + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) diff --git a/hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf new file mode 100644 index 000000000..f51792417 --- /dev/null +++ b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf @@ -0,0 +1,84 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} + +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} + +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + + output: + path "COLLECTED-output.txt" + + script: + """ + cat ${input_files} > 'COLLECTED-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect()) + + // optional view statements + convertToUpper.out.view { "Before collect: $it" } + convertToUpper.out.collect().view { "After collect: $it" } +} diff --git a/hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf new file mode 100644 index 000000000..65ac85ce0 --- /dev/null +++ b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf @@ -0,0 +1,86 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} + +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} + +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + val batch_name + + output: + path "COLLECTED-${batch_name}-output.txt" + + script: + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // optional view statements + convertToUpper.out.view { "Before collect: $it" } + convertToUpper.out.collect().view { "After collect: $it" } +} diff --git a/hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf new file mode 100644 index 000000000..92af832e7 --- /dev/null +++ b/hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf @@ -0,0 +1,91 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} + +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} + +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + val batch_name + + output: + path "COLLECTED-${batch_name}-output.txt" , emit: outfile + val count_greetings , emit: count + + script: + count_greetings = input_files.size() + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } + + // optional view statements + //convertToUpper.out.view { "Before collect: $it" } + //convertToUpper.out.collect().view { "After collect: $it" } +} diff --git a/hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf b/hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf new file mode 100644 index 000000000..0d384c479 --- /dev/null +++ b/hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf @@ -0,0 +1,71 @@ +#!/usr/bin/env nextflow + +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} + +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + val batch_name + + output: + path "COLLECTED-${batch_name}-output.txt" , emit: outfile + val count_greetings , emit: count + + script: + count_greetings = input_files.size() + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' + +// Include modules +include { sayHello } from './modules/sayHello.nf' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } +} diff --git a/hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf b/hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf new file mode 100644 index 000000000..e34edebed --- /dev/null +++ b/hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf @@ -0,0 +1,53 @@ +#!/usr/bin/env nextflow + +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + val batch_name + + output: + path "COLLECTED-${batch_name}-output.txt" , emit: outfile + val count_greetings , emit: count + + script: + count_greetings = input_files.size() + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +} + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' + +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } +} diff --git a/hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf b/hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf new file mode 100644 index 000000000..8764606bf --- /dev/null +++ b/hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf @@ -0,0 +1,32 @@ +#!/usr/bin/env nextflow + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' + +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' +include { collectGreetings } from './modules/collectGreetings.nf' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } +} diff --git a/hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf b/hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf new file mode 100644 index 000000000..849bba4b6 --- /dev/null +++ b/hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf @@ -0,0 +1,21 @@ +/* + * Collect uppercase greetings into a single output file + */ +process collectGreetings { + + publishDir 'results', mode: 'copy' + + input: + path input_files + val batch_name + + output: + path "COLLECTED-${batch_name}-output.txt" , emit: outfile + val count_greetings , emit: count + + script: + count_greetings = input_files.size() + """ + cat ${input_files} > 'COLLECTED-${batch_name}-output.txt' + """ +} diff --git a/hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf b/hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf new file mode 100644 index 000000000..b2689e8e9 --- /dev/null +++ b/hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf @@ -0,0 +1,20 @@ +#!/usr/bin/env nextflow + +/* + * Use a text replacement tool to convert the greeting to uppercase + */ +process convertToUpper { + + publishDir 'results', mode: 'copy' + + input: + path input_file + + output: + path "UPPER-${input_file}" + + script: + """ + cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + """ +} diff --git a/hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf b/hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf new file mode 100644 index 000000000..6005ad54c --- /dev/null +++ b/hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf @@ -0,0 +1,20 @@ +#!/usr/bin/env nextflow + +/* + * Use echo to print 'Hello World!' to a file + */ +process sayHello { + + publishDir 'results', mode: 'copy' + + input: + val greeting + + output: + path "${greeting}-output.txt" + + script: + """ + echo '$greeting' > '$greeting-output.txt' + """ +} diff --git a/hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf b/hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf new file mode 100644 index 000000000..f187831d1 --- /dev/null +++ b/hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf @@ -0,0 +1,37 @@ +#!/usr/bin/env nextflow + +/* + * Pipeline parameters + */ +params.greeting = 'greetings.csv' +params.batch = 'test-batch' +params.character = 'turkey' + +// Include modules +include { sayHello } from './modules/sayHello.nf' +include { convertToUpper } from './modules/convertToUpper.nf' +include { collectGreetings } from './modules/collectGreetings.nf' +include { cowpy } from './modules/cowpy.nf' + +workflow { + + // create a channel for inputs from a CSV file + greeting_ch = Channel.fromPath(params.greeting) + .splitCsv() + .map { line -> line[0] } + + // emit a greeting + sayHello(greeting_ch) + + // convert the greeting to uppercase + convertToUpper(sayHello.out) + + // collect all the greetings into one file + collectGreetings(convertToUpper.out.collect(), params.batch) + + // emit a message about the size of the batch + collectGreetings.out.count.view { "There were $it greetings in this batch" } + + // generate ASCII art of the greetings with cowpy + cowpy(collectGreetings.out.outfile, params.character) +} diff --git a/hello-nextflow/solutions/5-hello-containers/modules/cowpy.nf b/hello-nextflow/solutions/5-hello-containers/modules/cowpy.nf new file mode 100644 index 000000000..60b739b62 --- /dev/null +++ b/hello-nextflow/solutions/5-hello-containers/modules/cowpy.nf @@ -0,0 +1,21 @@ +#!/usr/bin/env nextflow + +// Generate ASCII art with cowpy (https://github.com/jeffbuttars/cowpy) +process cowpy { + + publishDir 'results', mode: 'copy' + + container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' + + input: + path input_file + val character + + output: + path "cowpy-${input_file}" + + script: + """ + cat $input_file | cowpy -c "$character" > cowpy-${input_file} + """ +} diff --git a/hello-nextflow/solutions/6-hello-config/modules/cowpy.nf b/hello-nextflow/solutions/6-hello-config/modules/cowpy.nf new file mode 100644 index 000000000..2bc7ed612 --- /dev/null +++ b/hello-nextflow/solutions/6-hello-config/modules/cowpy.nf @@ -0,0 +1,22 @@ +#!/usr/bin/env nextflow + +// Generate ASCII art with cowpy (https://github.com/jeffbuttars/cowpy) +process cowpy { + + publishDir 'results', mode: 'copy' + + container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' + conda 'conda-forge::cowpy==1.1.5' + + input: + path input_file + val character + + output: + path "cowpy-${input_file}" + + script: + """ + cat $input_file | cowpy -c "$character" > cowpy-${input_file} + """ +} diff --git a/hello-nextflow/solutions/6-hello-config/nextflow.config b/hello-nextflow/solutions/6-hello-config/nextflow.config new file mode 100644 index 000000000..0a5fd46b9 --- /dev/null +++ b/hello-nextflow/solutions/6-hello-config/nextflow.config @@ -0,0 +1 @@ +docker.enabled = false diff --git a/hello-nextflow/solutions/hello-config/1-nextflow.config b/hello-nextflow/solutions/hello-config/1-nextflow.config deleted file mode 100644 index 936de4924..000000000 --- a/hello-nextflow/solutions/hello-config/1-nextflow.config +++ /dev/null @@ -1,4 +0,0 @@ -docker.fixOwnership = true - -docker.enabled = false -conda.enabled = true diff --git a/hello-nextflow/solutions/hello-config/2-nextflow.config b/hello-nextflow/solutions/hello-config/2-nextflow.config deleted file mode 100644 index aa230a50e..000000000 --- a/hello-nextflow/solutions/hello-config/2-nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -docker.fixOwnership = true - -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } -} diff --git a/hello-nextflow/solutions/hello-config/3-nextflow.config b/hello-nextflow/solutions/hello-config/3-nextflow.config deleted file mode 100644 index 3de8546f9..000000000 --- a/hello-nextflow/solutions/hello-config/3-nextflow.config +++ /dev/null @@ -1,18 +0,0 @@ -docker.fixOwnership = true - -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - my_laptop { - process.executor = 'local' - docker.enabled = true - } - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - } -} diff --git a/hello-nextflow/solutions/hello-config/4-nextflow.config b/hello-nextflow/solutions/hello-config/4-nextflow.config deleted file mode 100644 index 5cb2778fa..000000000 --- a/hello-nextflow/solutions/hello-config/4-nextflow.config +++ /dev/null @@ -1,33 +0,0 @@ -docker.fixOwnership = true - -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - my_laptop { - process.executor = 'local' - docker.enabled = true - } - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - process.resourceLimits = [ - memory: 750.GB, - cpus: 200, - time: 30.d - ] - } -} - -process { - // defaults for all processes - cpus = 2 - memory = 2.GB - // allocations for a specific process - withName: 'GATK_JOINTGENOTYPING' { - cpus = 4 - } -} diff --git a/hello-nextflow/solutions/hello-config/5-nextflow.config b/hello-nextflow/solutions/hello-config/5-nextflow.config deleted file mode 100644 index 24d068339..000000000 --- a/hello-nextflow/solutions/hello-config/5-nextflow.config +++ /dev/null @@ -1,69 +0,0 @@ -docker.fixOwnership = true - - -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = null - - // Output directory - params.outdir = "results_genomics" - - // Accessory files - reference = null - reference_index = null - reference_dict = null - intervals = null - - // Base name for final output file - cohort_name = "my_cohort" -} - - -profiles { - docker_on { - docker.enabled = true - } - conda_on { - conda.enabled = true - } - my_laptop { - process.executor = 'local' - docker.enabled = true - } - univ_hpc { - process.executor = 'slurm' - conda.enabled = true - process.resourceLimits = [ - memory: 750.GB, - cpus: 200, - time: 30.d - ] - } - demo { - // Primary input (file of input files, one per line) - params.reads_bam = "data/sample_bams.txt" - - // Accessory files - params.reference = "data/ref/ref.fasta" - params.reference_index = "data/ref/ref.fasta.fai" - params.reference_dict = "data/ref/ref.dict" - params.intervals = "data/ref/intervals.bed" - - // Base name for final output file - params.cohort_name = "family_trio" - } -} - -process { - // defaults for all processes - cpus = 2 - memory = 2.GB - // allocations for a specific process - withName: 'GATK_JOINTGENOTYPING' { - cpus = 4 - } -} diff --git a/hello-nextflow/solutions/hello-config/final-main.nf b/hello-nextflow/solutions/hello-config/final-main.nf deleted file mode 100644 index 316b0c3a8..000000000 --- a/hello-nextflow/solutions/hello-config/final-main.nf +++ /dev/null @@ -1,133 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - conda "bioconda::samtools=1.20" - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} - -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" - path "${cohort_name}.joint.vcf.idx" - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) - - // Collect variant calling outputs across samples - all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect() - all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect() - - // Combine GVCFs into a GenomicsDB data store and apply joint genotyping - GATK_JOINTGENOTYPING( - all_gvcfs_ch, - all_idxs_ch, - intervals_file, - params.cohort_name, - ref_file, - ref_index_file, - ref_dict_file - ) -} diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf deleted file mode 100644 index c14945822..000000000 --- a/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input -params.reads_bam = "${projectDir}/data/bam/reads_mother.bam" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - path "${input_bam}.bai" - - script: - """ - samtools index '$input_bam' - """ -} - -workflow { - - // Create input channel (single file via CLI parameter) - reads_ch = Channel.fromPath(params.reads_bam) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) -} diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf deleted file mode 100644 index bb414c783..000000000 --- a/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf +++ /dev/null @@ -1,91 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input -params.reads_bam = "${projectDir}/data/bam/reads_mother.bam" - -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - path "${input_bam}.bai" - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - path input_bam_index - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.vcf" , emit: vcf - path "${input_bam}.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.vcf \ - -L ${interval_list} - """ -} - -workflow { - - // Create input channel (single file via CLI parameter) - reads_ch = Channel.fromPath(params.reads_bam) - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - reads_ch, - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) -} diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf deleted file mode 100644 index 3b38f252e..000000000 --- a/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf +++ /dev/null @@ -1,93 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input (array of three samples) -params.reads_bam = [ - "${projectDir}/data/bam/reads_mother.bam", - "${projectDir}/data/bam/reads_father.bam", - "${projectDir}/data/bam/reads_son.bam" -] - -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.vcf" , emit: vcf - path "${input_bam}.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.vcf \ - -L ${interval_list} - """ -} - -workflow { - - // Create input channel (single file via CLI parameter) - reads_ch = Channel.fromPath(params.reads_bam) - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) -} diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf deleted file mode 100644 index bb3b821a3..000000000 --- a/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input (file of input files, one per line) -params.reads_bam = "${projectDir}/data/sample_bams.txt" - -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.vcf" , emit: vcf - path "${input_bam}.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.vcf \ - -L ${interval_list} - """ -} - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) -} diff --git a/hello-nextflow/solutions/hello-modules/final-main.nf b/hello-nextflow/solutions/hello-modules/final-main.nf deleted file mode 100644 index 3e55a0d15..000000000 --- a/hello-nextflow/solutions/hello-modules/final-main.nf +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env nextflow - -// Include modules -include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf' -include { GATK_HAPLOTYPECALLER } from './modules/local/gatk/haplotypecaller/main.nf' -include { GATK_JOINTGENOTYPING } from './modules/local/gatk/jointgenotyping/main.nf' - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) - - // Collect variant calling outputs across samples - all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect() - all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect() - - // Combine GVCFs into a GenomicsDB data store and apply joint genotyping - GATK_JOINTGENOTYPING( - all_gvcfs_ch, - all_idxs_ch, - intervals_file, - params.cohort_name, - ref_file, - ref_index_file, - ref_dict_file - ) -} diff --git a/hello-nextflow/solutions/hello-modules/modules/local/gatk/haplotypecaller/main.nf b/hello-nextflow/solutions/hello-modules/modules/local/gatk/haplotypecaller/main.nf deleted file mode 100644 index 63c615daa..000000000 --- a/hello-nextflow/solutions/hello-modules/modules/local/gatk/haplotypecaller/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} diff --git a/hello-nextflow/solutions/hello-modules/modules/local/gatk/jointgenotyping/main.nf b/hello-nextflow/solutions/hello-modules/modules/local/gatk/jointgenotyping/main.nf deleted file mode 100644 index 3dad42be5..000000000 --- a/hello-nextflow/solutions/hello-modules/modules/local/gatk/jointgenotyping/main.nf +++ /dev/null @@ -1,38 +0,0 @@ -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" , emit: vcf - path "${cohort_name}.joint.vcf.idx", emit: idx - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} diff --git a/hello-nextflow/solutions/hello-modules/modules/local/samtools/index/main.nf b/hello-nextflow/solutions/hello-modules/modules/local/samtools/index/main.nf deleted file mode 100644 index 103a47631..000000000 --- a/hello-nextflow/solutions/hello-modules/modules/local/samtools/index/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - conda "bioconda::samtools=1.20" - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf deleted file mode 100644 index 63c615daa..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/tests/main.nf.test b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/tests/main.nf.test deleted file mode 100644 index 74d97e274..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/tests/main.nf.test +++ /dev/null @@ -1,111 +0,0 @@ -nextflow_process { - - name "Test Process GATK_HAPLOTYPECALLER" - script "../main.nf" - process "GATK_HAPLOTYPECALLER" - - test("reads_son [bam]") { - - setup { - run("SAMTOOLS_INDEX") { - script "../../../samtools/index/main.nf" - process { - """ - input[0] = file("${projectDir}/data/bam/reads_son.bam") - """ - } - } - } - - when { - params { - outdir = "tests/results" - } - process { - """ - input[0] = SAMTOOLS_INDEX.out - input[1] = file("${projectDir}/data/ref/ref.fasta") - input[2] = file("${projectDir}/data/ref/ref.fasta.fai") - input[3] = file("${projectDir}/data/ref/ref.dict") - input[4] = file("${projectDir}/data/ref/intervals.bed") - """ - } - } - - then { - assert process.success - assert path(process.out[0][0]).readLines().contains('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_son') - assert path(process.out[0][0]).readLines().contains('20_10037292_10066351 3277 . G . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,719') - } - - } - test("reads_mother [bam]") { - - setup { - run("SAMTOOLS_INDEX") { - script "../../../samtools/index/main.nf" - process { - """ - input[0] = file("${projectDir}/data/bam/reads_mother.bam") - """ - } - } - } - - when { - params { - outdir = "tests/results" - } - process { - """ - input[0] = SAMTOOLS_INDEX.out - input[1] = file("${projectDir}/data/ref/ref.fasta") - input[2] = file("${projectDir}/data/ref/ref.fasta.fai") - input[3] = file("${projectDir}/data/ref/ref.dict") - input[4] = file("${projectDir}/data/ref/intervals.bed") - """ - } - } - - then { - assert process.success - assert path(process.out[0][0]).readLines().contains('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_mother') - assert path(process.out[0][0]).readLines().contains('20_10037292_10066351 3277 . G . . END=3278 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530') - } - } - test("reads_father [bam]") { - - setup { - run("SAMTOOLS_INDEX") { - script "../../../samtools/index/main.nf" - process { - """ - input[0] = file("${projectDir}/data/bam/reads_father.bam") - """ - } - } - } - - when { - params { - outdir = "tests/results" - } - process { - """ - input[0] = SAMTOOLS_INDEX.out - input[1] = file("${projectDir}/data/ref/ref.fasta") - input[2] = file("${projectDir}/data/ref/ref.fasta.fai") - input[3] = file("${projectDir}/data/ref/ref.dict") - input[4] = file("${projectDir}/data/ref/intervals.bed") - """ - } - } - - then { - assert process.success - assert path(process.out[0][0]).readLines().contains('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_father') - assert path(process.out[0][0]).readLines().contains('20_10037292_10066351 3277 . G . . END=3281 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,120,1800') - } - } - -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/tests/main.nf.test.snap b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/tests/main.nf.test.snap deleted file mode 100644 index c56c44ee7..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/tests/main.nf.test.snap +++ /dev/null @@ -1,36 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "reads_son.bam.g.vcf:md5,2184752e8d3281646f4622aa518e88fd" - ], - "1": [ - "reads_son.bam.g.vcf.idx:md5,113b4c76d6d5b749825f278c7b1821ee" - ] - } - ], - "meta": { - "nf-test": "0.9.1", - "nextflow": "24.02.0" - }, - "timestamp": "2024-10-27T23:57:49.079801161" - }, - "reads_son [bam]": { - "content": [ - { - "0": [ - "reads_son.bam.g.vcf:md5,73e33550858a2cd8a602a0a9de22c1e5" - ], - "1": [ - "reads_son.bam.g.vcf.idx:md5,160fd200d8cd6044f3cb5da4246dc4fa" - ] - } - ], - "meta": { - "nf-test": "0.9.1", - "nextflow": "24.02.0" - }, - "timestamp": "2024-10-27T23:59:25.191508837" - } -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/main.nf b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/main.nf deleted file mode 100644 index 3dad42be5..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/main.nf +++ /dev/null @@ -1,38 +0,0 @@ -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - conda "bioconda::gatk4=4.5.0.0" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" , emit: vcf - path "${cohort_name}.joint.vcf.idx", emit: idx - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf deleted file mode 100644 index 6d9c40779..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf +++ /dev/null @@ -1,1379 +0,0 @@ -##fileformat=VCFv4.2 -##ALT= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) -##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) -##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) -##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) -##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) -##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) -##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) -##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) -##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) -##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) -##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) -##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) -##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) -##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) -##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) -##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) -##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) -##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) -##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) -##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) -##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) -##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) -##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) -##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) -##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) -##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) -##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) -##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) -##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) -##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) -##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) -##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) -##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) -##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) -##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) -##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) -##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) -##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) -##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) -##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) -##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) -##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) -##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) -##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) -##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) -##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) -##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) -##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) -##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) -##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) -##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) -##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) -##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) -##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) -##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) -##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) -##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) -##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) -##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) -##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) -##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) -##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) -##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) -##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) -##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive) -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_father -20_10037292_10066351 3277 . G . . END=3281 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,120,1800 -20_10037292_10066351 3282 . T . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:45:95:45:0,95,1267 -20_10037292_10066351 3283 . T . . END=3300 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,112,1375 -20_10037292_10066351 3301 . C . . END=3301 GT:DP:GQ:MIN_DP:PL 0/0:52:88:52:0,88,1492 -20_10037292_10066351 3302 . T . . END=3307 GT:DP:GQ:MIN_DP:PL 0/0:51:99:49:0,112,1471 -20_10037292_10066351 3308 . A . . END=3308 GT:DP:GQ:MIN_DP:PL 0/0:49:84:49:0,84,1399 -20_10037292_10066351 3309 . A . . END=3437 GT:DP:GQ:MIN_DP:PL 0/0:47:99:41:0,107,1349 -20_10037292_10066351 3438 . T . . END=3447 GT:DP:GQ:MIN_DP:PL 0/0:41:90:38:0,90,1108 -20_10037292_10066351 3448 . T . . END=3449 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 3450 . A . . END=3450 GT:DP:GQ:MIN_DP:PL 0/0:35:50:35:0,50,880 -20_10037292_10066351 3451 . C . . END=3451 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 3452 . C . . END=3452 GT:DP:GQ:MIN_DP:PL 0/0:36:68:36:0,68,1042 -20_10037292_10066351 3453 . T . . END=3453 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 3454 . G . . END=3454 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,948 -20_10037292_10066351 3455 . T . . END=3458 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 -20_10037292_10066351 3459 . T . . END=3460 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 3461 . C . . END=3461 GT:DP:GQ:MIN_DP:PL 0/0:39:57:39:0,57,992 -20_10037292_10066351 3462 . T . . END=3462 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,99,1485 -20_10037292_10066351 3463 . G . . END=3463 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,910 -20_10037292_10066351 3464 . T . . END=3468 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 3469 . C . . END=3469 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,939 -20_10037292_10066351 3470 . T . . END=3472 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 3473 . T . . END=3473 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1129 -20_10037292_10066351 3474 . T . . END=3474 GT:DP:GQ:MIN_DP:PL 0/0:38:92:38:0,92,1102 -20_10037292_10066351 3475 . C . . END=3475 GT:DP:GQ:MIN_DP:PL 0/0:38:63:38:0,63,957 -20_10037292_10066351 3476 . T . . END=3478 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1197 -20_10037292_10066351 3479 . T . . END=3479 GT:DP:GQ:MIN_DP:PL 0/0:41:92:41:0,92,1155 -20_10037292_10066351 3480 . C CT, 359.60 . BaseQRankSum=0.220;DP=32;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=115200,32;ReadPosRankSum=-1.147 GT:AD:DP:GQ:PL:SB 0/1:15,16,0:31:99:367,0,375,412,423,835:6,9,9,7 -20_10037292_10066351 3481 . T . . END=3482 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3483 . T . . END=3483 GT:DP:GQ:MIN_DP:PL 0/0:32:65:32:0,65,949 -20_10037292_10066351 3484 . T . . END=3484 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3485 . T . . END=3487 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3488 . T . . END=3489 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,889 -20_10037292_10066351 3490 . C . . END=3490 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 3491 . A . . END=3491 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,996 -20_10037292_10066351 3492 . A . . END=3494 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 3495 . T . . END=3495 GT:DP:GQ:MIN_DP:PL 0/0:35:60:35:0,60,952 -20_10037292_10066351 3496 . A . . END=3497 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 3498 . A . . END=3498 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,937 -20_10037292_10066351 3499 . C . . END=3499 GT:DP:GQ:MIN_DP:PL 0/0:29:86:29:0,86,758 -20_10037292_10066351 3500 . G . . END=3500 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,646 -20_10037292_10066351 3501 . T . . END=3504 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 3505 . A . . END=3505 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,913 -20_10037292_10066351 3506 . C . . END=3506 GT:DP:GQ:MIN_DP:PL 0/0:31:45:31:0,45,739 -20_10037292_10066351 3507 . T . . END=3511 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3512 . A . . END=3512 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,994 -20_10037292_10066351 3513 . A . . END=3517 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 3518 . C . . END=3519 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,885 -20_10037292_10066351 3520 . AT A, 288.60 . BaseQRankSum=1.033;DP=34;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=122400,34;ReadPosRankSum=0.701 GT:AD:DP:GQ:PL:SB 0/1:18,13,0:31:99:296,0,424,350,463,813:8,10,7,6 -20_10037292_10066351 3522 . T . . END=3543 GT:DP:GQ:MIN_DP:PL 0/0:50:99:44:0,112,1347 -20_10037292_10066351 3544 . A . . END=3544 GT:DP:GQ:MIN_DP:PL 0/0:49:89:49:0,89,1374 -20_10037292_10066351 3545 . C . . END=3615 GT:DP:GQ:MIN_DP:PL 0/0:50:99:44:0,113,1172 -20_10037292_10066351 3616 . A . . END=3616 GT:DP:GQ:MIN_DP:PL 0/0:45:84:45:0,84,1268 -20_10037292_10066351 3617 . T . . END=3698 GT:DP:GQ:MIN_DP:PL 0/0:44:99:37:0,104,1096 -20_10037292_10066351 3699 . A . . END=3699 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1090 -20_10037292_10066351 3700 . G . . END=3701 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1116 -20_10037292_10066351 3702 . A . . END=3702 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1137 -20_10037292_10066351 3703 . T . . END=3704 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 3705 . G . . END=3705 GT:DP:GQ:MIN_DP:PL 0/0:40:85:40:0,85,1190 -20_10037292_10066351 3706 . G . . END=3710 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,114,1710 -20_10037292_10066351 3711 . G . . END=3711 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1263 -20_10037292_10066351 3712 . G . . END=3749 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,114,1209 -20_10037292_10066351 3750 . A . . END=3750 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1191 -20_10037292_10066351 3751 . A . . END=3865 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,100,1137 -20_10037292_10066351 3866 . G . . END=3866 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1117 -20_10037292_10066351 3867 . G . . END=3867 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3868 . T . . END=3868 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1109 -20_10037292_10066351 3869 . G . . END=3869 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3870 . T . . END=3870 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1088 -20_10037292_10066351 3871 . A . . END=3871 GT:DP:GQ:MIN_DP:PL 0/0:38:68:38:0,68,1086 -20_10037292_10066351 3872 . C . . END=3951 GT:DP:GQ:MIN_DP:PL 0/0:47:99:36:0,108,1151 -20_10037292_10066351 3952 . T . . END=3952 GT:DP:GQ:MIN_DP:PL 0/0:46:89:46:0,89,1351 -20_10037292_10066351 3953 . G . . END=4011 GT:DP:GQ:MIN_DP:PL 0/0:48:99:46:0,120,1800 -20_10037292_10066351 4012 . C T, 1432.06 . DP=47;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=169200,47 GT:AD:DP:GQ:PL:SB 1/1:0,46,0:46:99:1446,137,0,1446,137,1446:0,0,23,23 -20_10037292_10066351 4013 . G . . END=4035 GT:DP:GQ:MIN_DP:PL 0/0:48:99:42:0,108,1267 -20_10037292_10066351 4036 . T . . END=4036 GT:DP:GQ:MIN_DP:PL 0/0:43:95:43:0,95,1242 -20_10037292_10066351 4037 . T . . END=4060 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,104,1268 -20_10037292_10066351 4061 . A . . END=4061 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1217 -20_10037292_10066351 4062 . A . . END=4078 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,108,1620 -20_10037292_10066351 4079 . C . . END=4079 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1207 -20_10037292_10066351 4080 . A . . END=4121 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1157 -20_10037292_10066351 4122 . G . . END=4122 GT:DP:GQ:MIN_DP:PL 0/0:38:90:38:0,90,1137 -20_10037292_10066351 4123 . G . . END=4123 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 4124 . G . . END=4125 GT:DP:GQ:MIN_DP:PL 0/0:39:92:38:0,92,1088 -20_10037292_10066351 4126 . C . . END=4129 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,105,1575 -20_10037292_10066351 4130 . A . . END=4130 GT:DP:GQ:MIN_DP:PL 0/0:37:86:37:0,86,1018 -20_10037292_10066351 4131 . C . . END=4154 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1046 -20_10037292_10066351 4155 . T . . END=4155 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1137 -20_10037292_10066351 4156 . A . . END=4163 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1181 -20_10037292_10066351 4164 . T . . END=4164 GT:DP:GQ:MIN_DP:PL 0/0:40:97:40:0,97,1234 -20_10037292_10066351 4165 . A . . END=4177 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1088 -20_10037292_10066351 4178 . A . . END=4178 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1165 -20_10037292_10066351 4179 . T . . END=4198 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,99,1182 -20_10037292_10066351 4199 . G . . END=4201 GT:DP:GQ:MIN_DP:PL 0/0:39:96:37:0,96,1440 -20_10037292_10066351 4202 . G . . END=4204 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 4205 . T . . END=4217 GT:DP:GQ:MIN_DP:PL 0/0:34:93:32:0,93,1395 -20_10037292_10066351 4218 . G . . END=4218 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1030 -20_10037292_10066351 4219 . A . . END=4219 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 4220 . T . . END=4238 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1350 -20_10037292_10066351 4239 . C . . END=4240 GT:DP:GQ:MIN_DP:PL 0/0:34:66:33:0,66,924 -20_10037292_10066351 4241 . T . . END=4241 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 4242 . G . . END=4242 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,1040 -20_10037292_10066351 4243 . G . . END=4243 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,952 -20_10037292_10066351 4244 . T . . END=4244 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 4245 . T . . END=4245 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,968 -20_10037292_10066351 4246 . G . . END=4247 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 4248 . T . . END=4249 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,932 -20_10037292_10066351 4250 . G . . END=4250 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 4251 . T . . END=4252 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,904 -20_10037292_10066351 4253 . A . . END=4258 GT:DP:GQ:MIN_DP:PL 0/0:35:71:33:0,71,1001 -20_10037292_10066351 4259 . T . . END=4259 GT:DP:GQ:MIN_DP:PL 0/0:36:57:36:0,57,1051 -20_10037292_10066351 4260 . G . . END=4260 GT:DP:GQ:MIN_DP:PL 0/0:37:41:37:0,41,993 -20_10037292_10066351 4261 . G . . END=4261 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 4262 . T . . END=4263 GT:DP:GQ:MIN_DP:PL 0/0:36:71:35:0,71,1014 -20_10037292_10066351 4264 . T . . END=4264 GT:DP:GQ:MIN_DP:PL 0/0:37:62:37:0,62,1075 -20_10037292_10066351 4265 . G . . END=4265 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1050 -20_10037292_10066351 4266 . T . . END=4267 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1073 -20_10037292_10066351 4268 . T . . END=4271 GT:DP:GQ:MIN_DP:PL 0/0:37:75:37:0,75,1020 -20_10037292_10066351 4272 . A . . END=4272 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1090 -20_10037292_10066351 4273 . C . . END=4273 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1032 -20_10037292_10066351 4274 . C . . END=4274 GT:DP:GQ:MIN_DP:PL 0/0:38:48:38:0,48,1047 -20_10037292_10066351 4275 . A . . END=4287 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 4288 . T . . END=4288 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1099 -20_10037292_10066351 4289 . A . . END=4289 GT:DP:GQ:MIN_DP:PL 0/0:36:45:36:0,45,916 -20_10037292_10066351 4290 . T . . END=4290 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1107 -20_10037292_10066351 4291 . C . . END=4292 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4293 . G . . END=4293 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1065 -20_10037292_10066351 4294 . A . . END=4299 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4300 . G . . END=4304 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1058 -20_10037292_10066351 4305 . A . . END=4307 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 4308 . A . . END=4308 GT:DP:GQ:MIN_DP:PL 0/0:39:89:39:0,89,1179 -20_10037292_10066351 4309 . G . . END=4311 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 4312 . G . . END=4312 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1067 -20_10037292_10066351 4313 . G . . END=4318 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1130 -20_10037292_10066351 4319 . G . . END=4319 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1257 -20_10037292_10066351 4320 . A . . END=4326 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,105,1575 -20_10037292_10066351 4327 . A . . END=4327 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1145 -20_10037292_10066351 4328 . A . . END=4329 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,106,1200 -20_10037292_10066351 4330 . G . . END=4330 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1128 -20_10037292_10066351 4331 . A . . END=4334 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,107,1132 -20_10037292_10066351 4335 . A . . END=4336 GT:DP:GQ:MIN_DP:PL 0/0:38:94:38:0,94,1187 -20_10037292_10066351 4337 . A . . END=4337 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,114,1096 -20_10037292_10066351 4338 . C . . END=4338 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1117 -20_10037292_10066351 4339 . C . . END=4358 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,99,1173 -20_10037292_10066351 4359 . A . . END=4359 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1130 -20_10037292_10066351 4360 . G . . END=4360 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1244 -20_10037292_10066351 4361 . G . . END=4373 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,106,1101 -20_10037292_10066351 4374 . G . . END=4374 GT:DP:GQ:MIN_DP:PL 0/0:39:74:39:0,74,1076 -20_10037292_10066351 4375 . A . . END=4375 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1081 -20_10037292_10066351 4376 . T . . END=4380 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1077 -20_10037292_10066351 4381 . T . . END=4381 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1076 -20_10037292_10066351 4382 . T . . END=4382 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,101,1117 -20_10037292_10066351 4383 . T . . END=4383 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1096 -20_10037292_10066351 4384 . C . . END=4384 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1028 -20_10037292_10066351 4385 . A . . END=4385 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1150 -20_10037292_10066351 4386 . G . . END=4386 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1053 -20_10037292_10066351 4387 . A . . END=4387 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 4388 . C . . END=4388 GT:DP:GQ:MIN_DP:PL 0/0:39:78:39:0,78,1010 -20_10037292_10066351 4389 . C . . END=4394 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,983 -20_10037292_10066351 4395 . A . . END=4395 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1120 -20_10037292_10066351 4396 . G . . END=4403 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,107,1141 -20_10037292_10066351 4404 . A . . END=4404 GT:DP:GQ:MIN_DP:PL 0/0:42:59:42:0,59,935 -20_10037292_10066351 4405 . A . . END=4405 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,114,1710 -20_10037292_10066351 4406 . C . . END=4406 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 4407 . A . . END=4408 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,939 -20_10037292_10066351 4409 . A ATG,ATATG, 955.03 . DP=34;ExcessHet=0.0000;MLEAC=0,2,0;MLEAF=0.00,1.00,0.00;RAW_MQandDP=122400,34 GT:AD:DP:GQ:PL:SB 2/2:0,0,28,0:28:90:969,998,1257,90,96,0,1003,1147,100,1113:0,0,9,19 -20_10037292_10066351 4410 . T . . END=4423 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 4424 . T . . END=4424 GT:DP:GQ:MIN_DP:PL 0/0:32:72:32:0,72,959 -20_10037292_10066351 4425 . G . . END=4431 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4432 . T . . END=4432 GT:DP:GQ:MIN_DP:PL 0/0:32:65:32:0,65,948 -20_10037292_10066351 4433 . G . . END=4435 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 4436 . C . . END=4436 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,943 -20_10037292_10066351 4437 . A . . END=4437 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4438 . T . . END=4443 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 4444 . T . . END=4450 GT:DP:GQ:MIN_DP:PL 0/0:33:84:28:0,84,723 -20_10037292_10066351 4451 . G . . END=4451 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 4452 . T . . END=4459 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 4460 . T . . END=4460 GT:DP:GQ:MIN_DP:PL 0/0:32:75:32:0,75,1125 -20_10037292_10066351 4461 . A . . END=4461 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 4462 . T . . END=4463 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 4464 . T TA, 621.60 . BaseQRankSum=0.108;DP=33;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=118800,33;ReadPosRankSum=1.266 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:15,17,0:32:99:0|1:4464_T_TA:629,0,554,674,605,1280:4464:6,9,6,11 -20_10037292_10066351 4465 . T TA, 621.60 . BaseQRankSum=-0.225;DP=32;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=115200,32;ReadPosRankSum=0.910 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:15,17,0:32:99:0|1:4464_T_TA:629,0,554,674,605,1280:4464:6,9,6,11 -20_10037292_10066351 4466 . T . . END=4467 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 4468 . T . . END=4472 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,1485 -20_10037292_10066351 4473 . G . . END=4473 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1021 -20_10037292_10066351 4474 . A . . END=4476 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,105,994 -20_10037292_10066351 4477 . C . . END=4477 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,963 -20_10037292_10066351 4478 . A . . END=4481 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1046 -20_10037292_10066351 4482 . T . . END=4492 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,981 -20_10037292_10066351 4493 . G . . END=4495 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,945 -20_10037292_10066351 4496 . G . . END=4496 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4497 . T . . END=4503 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 -20_10037292_10066351 4504 . A . . END=4504 GT:DP:GQ:MIN_DP:PL 0/0:30:61:30:0,61,825 -20_10037292_10066351 4505 . T . . END=4512 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4513 . C . . END=4514 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,812 -20_10037292_10066351 4515 . T . . END=4519 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 4520 . A . . END=4520 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,822 -20_10037292_10066351 4521 . C . . END=4521 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,799 -20_10037292_10066351 4522 . C . . END=4524 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 4525 . C . . END=4533 GT:DP:GQ:MIN_DP:PL 0/0:27:62:25:0,62,779 -20_10037292_10066351 4534 . G . . END=4534 GT:DP:GQ:MIN_DP:PL 0/0:25:57:25:0,57,722 -20_10037292_10066351 4535 . G . . END=4535 GT:DP:GQ:MIN_DP:PL 0/0:25:63:25:0,63,945 -20_10037292_10066351 4536 . T . . END=4541 GT:DP:GQ:MIN_DP:PL 0/0:23:57:22:0,57,855 -20_10037292_10066351 4542 . A . . END=4544 GT:DP:GQ:MIN_DP:PL 0/0:24:63:24:0,63,945 -20_10037292_10066351 4545 . T . . END=4545 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,644 -20_10037292_10066351 4546 . T . . END=4550 GT:DP:GQ:MIN_DP:PL 0/0:24:61:23:0,61,673 -20_10037292_10066351 4551 . T . . END=4551 GT:DP:GQ:MIN_DP:PL 0/0:25:42:25:0,42,739 -20_10037292_10066351 4552 . G . . END=4563 GT:DP:GQ:MIN_DP:PL 0/0:24:69:23:0,69,660 -20_10037292_10066351 4564 . C . . END=4564 GT:DP:GQ:MIN_DP:PL 0/0:22:48:22:0,48,565 -20_10037292_10066351 4565 . G . . END=4567 GT:DP:GQ:MIN_DP:PL 0/0:24:63:22:0,63,580 -20_10037292_10066351 4568 . T . . END=4568 GT:DP:GQ:MIN_DP:PL 0/0:24:59:24:0,59,679 -20_10037292_10066351 4569 . T . . END=4572 GT:DP:GQ:MIN_DP:PL 0/0:25:61:24:0,61,691 -20_10037292_10066351 4573 . G . . END=4573 GT:DP:GQ:MIN_DP:PL 0/0:25:45:25:0,45,636 -20_10037292_10066351 4574 . T . . END=4577 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,731 -20_10037292_10066351 4578 . T . . END=4584 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,692 -20_10037292_10066351 4585 . G . . END=4585 GT:DP:GQ:MIN_DP:PL 0/0:23:69:23:0,69,678 -20_10037292_10066351 4586 . A . . END=4586 GT:DP:GQ:MIN_DP:PL 0/0:24:53:24:0,53,694 -20_10037292_10066351 4587 . G . . END=4604 GT:DP:GQ:MIN_DP:PL 0/0:24:60:24:0,60,642 -20_10037292_10066351 4605 . T . . END=4605 GT:DP:GQ:MIN_DP:PL 0/0:24:54:24:0,54,810 -20_10037292_10066351 4606 . G . . END=4609 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 -20_10037292_10066351 4610 . A . . END=4612 GT:DP:GQ:MIN_DP:PL 0/0:24:54:21:0,54,810 -20_10037292_10066351 4613 . C . . END=4613 GT:DP:GQ:MIN_DP:PL 0/0:22:50:22:0,50,605 -20_10037292_10066351 4614 . T . . END=4616 GT:DP:GQ:MIN_DP:PL 0/0:23:54:21:0,54,810 -20_10037292_10066351 4617 . T . . END=4617 GT:DP:GQ:MIN_DP:PL 0/0:21:49:21:0,49,590 -20_10037292_10066351 4618 . C . . END=4618 GT:DP:GQ:MIN_DP:PL 0/0:21:36:21:0,36,562 -20_10037292_10066351 4619 . T . . END=4619 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 -20_10037292_10066351 4620 . C . . END=4620 GT:DP:GQ:MIN_DP:PL 0/0:19:37:19:0,37,499 -20_10037292_10066351 4621 . G . . END=4626 GT:DP:GQ:MIN_DP:PL 0/0:19:54:18:0,54,532 -20_10037292_10066351 4627 . C . . END=4627 GT:DP:GQ:MIN_DP:PL 0/0:19:24:19:0,24,493 -20_10037292_10066351 4628 . T . . END=4628 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20_10037292_10066351 4629 . G . . END=4629 GT:DP:GQ:MIN_DP:PL 0/0:19:42:19:0,42,568 -20_10037292_10066351 4630 . A . . END=4631 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20_10037292_10066351 4632 . C . . END=4632 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 -20_10037292_10066351 4633 . T . . END=4633 GT:DP:GQ:MIN_DP:PL 0/0:20:48:20:0,48,592 -20_10037292_10066351 4634 . C . . END=4634 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 -20_10037292_10066351 4635 . A . . END=4638 GT:DP:GQ:MIN_DP:PL 0/0:24:66:23:0,66,990 -20_10037292_10066351 4639 . G . . END=4639 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,667 -20_10037292_10066351 4640 . A . . END=4641 GT:DP:GQ:MIN_DP:PL 0/0:23:56:23:0,56,654 -20_10037292_10066351 4642 . C . . END=4644 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4645 . C . . END=4649 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,763 -20_10037292_10066351 4650 . T . . END=4650 GT:DP:GQ:MIN_DP:PL 0/0:26:64:26:0,64,757 -20_10037292_10066351 4651 . T . . END=4657 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 4658 . C . . END=4658 GT:DP:GQ:MIN_DP:PL 0/0:26:61:26:0,61,781 -20_10037292_10066351 4659 . C . . END=4660 GT:DP:GQ:MIN_DP:PL 0/0:28:80:27:0,80,793 -20_10037292_10066351 4661 . A . . END=4661 GT:DP:GQ:MIN_DP:PL 0/0:28:73:28:0,73,846 -20_10037292_10066351 4662 . A . . END=4664 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,870 -20_10037292_10066351 4665 . T . . END=4665 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,787 -20_10037292_10066351 4666 . A . . END=4666 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,793 -20_10037292_10066351 4667 . C . . END=4670 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,917 -20_10037292_10066351 4671 . G . . END=4671 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,880 -20_10037292_10066351 4672 . A . . END=4679 GT:DP:GQ:MIN_DP:PL 0/0:30:87:29:0,87,909 -20_10037292_10066351 4680 . T . . END=4680 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,985 -20_10037292_10066351 4681 . G . . END=4681 GT:DP:GQ:MIN_DP:PL 0/0:31:65:31:0,65,862 -20_10037292_10066351 4682 . T . . END=4682 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,981 -20_10037292_10066351 4683 . G . . END=4683 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,948 -20_10037292_10066351 4684 . A . . END=4691 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 4692 . C . . END=4697 GT:DP:GQ:MIN_DP:PL 0/0:29:78:27:0,78,1170 -20_10037292_10066351 4698 . G . . END=4701 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 4702 . T . . END=4706 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,928 -20_10037292_10066351 4707 . A . . END=4720 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,921 -20_10037292_10066351 4721 . T . . END=4721 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,937 -20_10037292_10066351 4722 . C . . END=4727 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 4728 . A . . END=4734 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 4735 . T . . END=4735 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1021 -20_10037292_10066351 4736 . A . . END=4736 GT:DP:GQ:MIN_DP:PL 0/0:33:70:33:0,70,940 -20_10037292_10066351 4737 . C . . END=4739 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 4740 . T . . END=4740 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,989 -20_10037292_10066351 4741 . A . . END=4745 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 4746 . G . . END=4754 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4755 . A . . END=4755 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,991 -20_10037292_10066351 4756 . A . . END=4760 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 4761 . A . . END=4761 GT:DP:GQ:MIN_DP:PL 0/0:37:74:37:0,74,1046 -20_10037292_10066351 4762 . G . . END=4762 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1043 -20_10037292_10066351 4763 . A . . END=4768 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1087 -20_10037292_10066351 4769 . G . . END=4769 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1036 -20_10037292_10066351 4770 . A . . END=4772 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 4773 . A . . END=4774 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1041 -20_10037292_10066351 4775 . T . . END=4775 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 4776 . C . . END=4778 GT:DP:GQ:MIN_DP:PL 0/0:39:96:38:0,96,1440 -20_10037292_10066351 4779 . T . . END=4779 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 4780 . A . . END=4780 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 4781 . T . . END=4789 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1485 -20_10037292_10066351 4790 . A . . END=4791 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 4792 . A . . END=4807 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1070 -20_10037292_10066351 4808 . C . . END=4808 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1087 -20_10037292_10066351 4809 . A . . END=4810 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1167 -20_10037292_10066351 4811 . T . . END=4811 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1048 -20_10037292_10066351 4812 . A . . END=4817 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4818 . C . . END=4818 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1096 -20_10037292_10066351 4819 . C . . END=4855 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,102,1195 -20_10037292_10066351 4856 . T . . END=4856 GT:DP:GQ:MIN_DP:PL 0/0:44:90:44:0,90,1268 -20_10037292_10066351 4857 . A . . END=4893 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,99,1256 -20_10037292_10066351 4894 . C . . END=4894 GT:DP:GQ:MIN_DP:PL 0/0:44:83:44:0,83,1313 -20_10037292_10066351 4895 . T . . END=4974 GT:DP:GQ:MIN_DP:PL 0/0:44:99:40:0,107,1201 -20_10037292_10066351 4975 . T . . END=4975 GT:DP:GQ:MIN_DP:PL 0/0:43:81:43:0,81,1251 -20_10037292_10066351 4976 . A . . END=4986 GT:DP:GQ:MIN_DP:PL 0/0:43:99:39:0,105,1575 -20_10037292_10066351 4987 . A . . END=4990 GT:DP:GQ:MIN_DP:PL 0/0:38:93:37:0,93,1395 -20_10037292_10066351 4991 . C . . END=4992 GT:DP:GQ:MIN_DP:PL 0/0:37:87:36:0,87,1305 -20_10037292_10066351 4993 . G . . END=4994 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 4995 . G . . END=4995 GT:DP:GQ:MIN_DP:PL 0/0:36:89:36:0,89,1095 -20_10037292_10066351 4996 . G . . END=5001 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 5002 . T . . END=5002 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,916 -20_10037292_10066351 5003 . T . . END=5005 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 5006 . G . . END=5006 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1068 -20_10037292_10066351 5007 . A . . END=5008 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 5009 . C . . END=5016 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5017 . G . . END=5017 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 5018 . G . . END=5026 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 5027 . C T, 1150.06 . DP=37;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=133200,37 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:1164,108,0,1164,108,1164:0,0,19,17 -20_10037292_10066351 5028 . C . . END=5034 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1206 -20_10037292_10066351 5035 . A . . END=5035 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1168 -20_10037292_10066351 5036 . T . . END=5045 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1179 -20_10037292_10066351 5046 . A . . END=5046 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1162 -20_10037292_10066351 5047 . G . . END=5055 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,101,1171 -20_10037292_10066351 5056 . G . . END=5056 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1102 -20_10037292_10066351 5057 . A . . END=5058 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1142 -20_10037292_10066351 5059 . G . . END=5061 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1117 -20_10037292_10066351 5062 . T . . END=5064 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 5065 . A . . END=5065 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1130 -20_10037292_10066351 5066 . A . . END=5066 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 5067 . C . . END=5067 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1147 -20_10037292_10066351 5068 . C . . END=5068 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,111,1665 -20_10037292_10066351 5069 . A . . END=5071 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1159 -20_10037292_10066351 5072 . G . . END=5072 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,103,1233 -20_10037292_10066351 5073 . A . . END=5073 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1186 -20_10037292_10066351 5074 . G . . END=5074 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,101,1226 -20_10037292_10066351 5075 . G . . END=5075 GT:DP:GQ:MIN_DP:PL 0/0:40:75:40:0,75,1121 -20_10037292_10066351 5076 . T . . END=5079 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,104,1188 -20_10037292_10066351 5080 . T . . END=5080 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1172 -20_10037292_10066351 5081 . C . . END=5125 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,102,1196 -20_10037292_10066351 5126 . A . . END=5126 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1147 -20_10037292_10066351 5127 . G . . END=5127 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 5128 . T . . END=5128 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1099 -20_10037292_10066351 5129 . C . . END=5187 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1143 -20_10037292_10066351 5188 . G . . END=5188 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1135 -20_10037292_10066351 5189 . G . . END=5190 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1149 -20_10037292_10066351 5191 . G . . END=5191 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1167 -20_10037292_10066351 5192 . G . . END=5193 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,111,1665 -20_10037292_10066351 5194 . T . . END=5194 GT:DP:GQ:MIN_DP:PL 0/0:39:85:39:0,85,1200 -20_10037292_10066351 5195 . C . . END=5228 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,102,1180 -20_10037292_10066351 5229 . T . . END=5229 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1052 -20_10037292_10066351 5230 . A . . END=5237 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,102,1168 -20_10037292_10066351 5238 . G . . END=5238 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1187 -20_10037292_10066351 5239 . C . . END=5249 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 5250 . A . . END=5254 GT:DP:GQ:MIN_DP:PL 0/0:37:96:35:0,96,1440 -20_10037292_10066351 5255 . C . . END=5262 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5263 . T . . END=5263 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,998 -20_10037292_10066351 5264 . G . . END=5271 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1013 -20_10037292_10066351 5272 . C . . END=5275 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 5276 . T . . END=5278 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5279 . T . . END=5281 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,983 -20_10037292_10066351 5282 . A . . END=5315 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,99,1161 -20_10037292_10066351 5316 . A . . END=5323 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 5324 . C . . END=5324 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1014 -20_10037292_10066351 5325 . A . . END=5334 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 5335 . G . . END=5337 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,992 -20_10037292_10066351 5338 . C . . END=5341 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 5342 . G . . END=5342 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,954 -20_10037292_10066351 5343 . T . . END=5344 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,1005 -20_10037292_10066351 5345 . C . . END=5345 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,988 -20_10037292_10066351 5346 . A . . END=5346 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1105 -20_10037292_10066351 5347 . G . . END=5347 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 5348 . G . . END=5349 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1004 -20_10037292_10066351 5350 . G . . END=5350 GT:DP:GQ:MIN_DP:PL 0/0:34:52:34:0,52,932 -20_10037292_10066351 5351 . C . . END=5351 GT:DP:GQ:MIN_DP:PL 0/0:34:46:34:0,46,977 -20_10037292_10066351 5352 . A . . END=5353 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1000 -20_10037292_10066351 5354 . A . . END=5354 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1002 -20_10037292_10066351 5355 . A . . END=5355 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5356 . T . . END=5358 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 5359 . C . . END=5359 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1003 -20_10037292_10066351 5360 . A . . END=5361 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1086 -20_10037292_10066351 5362 . A . . END=5364 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 5365 . G . . END=5365 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1083 -20_10037292_10066351 5366 . T . . END=5366 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 5367 . G . . END=5367 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 5368 . A . . END=5369 GT:DP:GQ:MIN_DP:PL 0/0:35:85:34:0,85,965 -20_10037292_10066351 5370 . T . . END=5370 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 5371 . C . . END=5371 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1033 -20_10037292_10066351 5372 . C . . END=5372 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,980 -20_10037292_10066351 5373 . T . . END=5374 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 5375 . G . . END=5376 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 5377 . G . . END=5383 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,937 -20_10037292_10066351 5384 . T . . END=5388 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,888 -20_10037292_10066351 5389 . T . . END=5394 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 5395 . A . . END=5395 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,896 -20_10037292_10066351 5396 . C . . END=5400 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 5401 . T . . END=5401 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,835 -20_10037292_10066351 5402 . T . . END=5402 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 5403 . T . . END=5403 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,901 -20_10037292_10066351 5404 . T . . END=5404 GT:DP:GQ:MIN_DP:PL 0/0:31:68:31:0,68,872 -20_10037292_10066351 5405 . T . . END=5405 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 5406 . A . . END=5406 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,986 -20_10037292_10066351 5407 . A . . END=5417 GT:DP:GQ:MIN_DP:PL 0/0:39:99:34:0,99,1485 -20_10037292_10066351 5418 . A . . END=5418 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 5419 . A . . END=5419 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1140 -20_10037292_10066351 5420 . C . . END=5422 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 5423 . C . . END=5435 GT:DP:GQ:MIN_DP:PL 0/0:40:99:36:0,99,1485 -20_10037292_10066351 5436 . A . . END=5436 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1058 -20_10037292_10066351 5437 . A . . END=5437 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1088 -20_10037292_10066351 5438 . C . . END=5440 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 5441 . G . . END=5441 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1044 -20_10037292_10066351 5442 . C . . END=5442 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 5443 . C . . END=5443 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1064 -20_10037292_10066351 5444 . T . . END=5446 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5447 . T . . END=5447 GT:DP:GQ:MIN_DP:PL 0/0:37:89:37:0,89,1070 -20_10037292_10066351 5448 . T . . END=5453 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 5454 . G . . END=5454 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1131 -20_10037292_10066351 5455 . A . . END=5468 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,105,1273 -20_10037292_10066351 5469 . A G, 545.64 . BaseQRankSum=-3.665;DP=42;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=151200,42;ReadPosRankSum=1.500 GT:AD:DP:GQ:PL:SB 0/1:18,23,0:41:99:553,0,486,607,555,1162:12,6,14,9 -20_10037292_10066351 5470 . G . . END=5486 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,117,1755 -20_10037292_10066351 5487 . A . . END=5487 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1225 -20_10037292_10066351 5488 . A . . END=5495 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1203 -20_10037292_10066351 7536 . C . . END=7551 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,1485 -20_10037292_10066351 7552 . T . . END=7552 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1073 -20_10037292_10066351 7553 . A . . END=7555 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 7556 . C . . END=7556 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,991 -20_10037292_10066351 7557 . A G, 305.64 . BaseQRankSum=-1.362;DP=37;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=133200,37;ReadPosRankSum=1.111 GT:AD:DP:GQ:PL:SB 0/1:19,15,0:34:99:313,0,493,370,538,907:11,8,8,7 -20_10037292_10066351 7558 . C . . END=7558 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 7559 . T . . END=7578 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1485 -20_10037292_10066351 7579 . T . . END=7579 GT:DP:GQ:MIN_DP:PL 0/0:38:92:38:0,92,1186 -20_10037292_10066351 7580 . C . . END=7582 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 7583 . C . . END=7583 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1177 -20_10037292_10066351 7584 . A . . END=7586 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 7587 . T . . END=7587 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1163 -20_10037292_10066351 7588 . T . . END=7599 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,100,1167 -20_10037292_10066351 7600 . C . . END=7600 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1131 -20_10037292_10066351 7601 . C . . END=7612 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,101,1205 -20_10037292_10066351 7613 . T . . END=7613 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1175 -20_10037292_10066351 7614 . C . . END=7617 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,111,1229 -20_10037292_10066351 7618 . G . . END=7618 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1191 -20_10037292_10066351 7619 . T . . END=7619 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 7620 . A . . END=7620 GT:DP:GQ:MIN_DP:PL 0/0:38:92:38:0,92,1159 -20_10037292_10066351 7621 . T . . END=7621 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1233 -20_10037292_10066351 7622 . A . . END=7622 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1202 -20_10037292_10066351 7623 . T . . END=7634 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1213 -20_10037292_10066351 7635 . G . . END=7635 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1213 -20_10037292_10066351 7636 . G . . END=7640 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,105,1575 -20_10037292_10066351 7641 . T . . END=7641 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1158 -20_10037292_10066351 7642 . T . . END=7643 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 7644 . A . . END=7644 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1085 -20_10037292_10066351 7645 . T . . END=7652 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,105,1140 -20_10037292_10066351 7653 . A . . END=7653 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 7654 . G . . END=7656 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 7657 . A . . END=7661 GT:DP:GQ:MIN_DP:PL 0/0:39:93:39:0,93,1395 -20_10037292_10066351 7662 . G . . END=7666 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 7667 . A . . END=7667 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,992 -20_10037292_10066351 7668 . C . . END=7681 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1088 -20_10037292_10066351 7682 . C . . END=7682 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1110 -20_10037292_10066351 7683 . C . . END=7689 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1530 -20_10037292_10066351 7690 . A . . END=7690 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1015 -20_10037292_10066351 7691 . C . . END=7700 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 7701 . A . . END=7705 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 7706 . C . . END=7706 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1305 -20_10037292_10066351 7707 . A . . END=7713 GT:DP:GQ:MIN_DP:PL 0/0:37:90:34:0,90,1350 -20_10037292_10066351 7714 . A . . END=7714 GT:DP:GQ:MIN_DP:PL 0/0:36:89:36:0,89,1115 -20_10037292_10066351 7715 . C . . END=7715 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 7716 . A . . END=7716 GT:DP:GQ:MIN_DP:PL 0/0:36:89:36:0,89,1160 -20_10037292_10066351 7717 . G . . END=7717 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7718 . T . . END=7719 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 7720 . C . . END=7720 GT:DP:GQ:MIN_DP:PL 0/0:34:83:34:0,83,1055 -20_10037292_10066351 7721 . T . . END=7722 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 7723 . A . . END=7723 GT:DP:GQ:MIN_DP:PL 0/0:34:66:34:0,66,975 -20_10037292_10066351 7724 . A . . END=7724 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,1060 -20_10037292_10066351 7725 . C . . END=7725 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7726 . A . . END=7726 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1088 -20_10037292_10066351 7727 . A . . END=7728 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1073 -20_10037292_10066351 7729 . G . . END=7729 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1042 -20_10037292_10066351 7730 . T . . END=7731 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 7732 . G . . END=7732 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1019 -20_10037292_10066351 7733 . A . . END=7740 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 7741 . A . . END=7745 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 7746 . G . . END=7748 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,979 -20_10037292_10066351 7749 . T . . END=7750 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1024 -20_10037292_10066351 7751 . C . . END=7751 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,992 -20_10037292_10066351 7752 . C . . END=7753 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 7754 . C . . END=7754 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,964 -20_10037292_10066351 7755 . C . . END=7755 GT:DP:GQ:MIN_DP:PL 0/0:33:58:33:0,58,922 -20_10037292_10066351 7756 . A . . END=7761 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 7762 . A . . END=7762 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,973 -20_10037292_10066351 7763 . T . . END=7767 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,888 -20_10037292_10066351 7768 . A . . END=7769 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7770 . C . . END=7771 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1081 -20_10037292_10066351 7772 . T . . END=7776 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1120 -20_10037292_10066351 7777 . T . . END=7777 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1094 -20_10037292_10066351 7778 . A . . END=7785 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1159 -20_10037292_10066351 7786 . G T, 1052.06 . DP=35;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=126000,35 GT:AD:DP:GQ:PL:SB 1/1:0,34,0:34:99:1066,102,0,1066,102,1066:0,0,8,26 -20_10037292_10066351 7787 . C . . END=7788 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 7789 . C . . END=7789 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1118 -20_10037292_10066351 7790 . A . . END=7790 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,111,1665 -20_10037292_10066351 7791 . T . . END=7791 GT:DP:GQ:MIN_DP:PL 0/0:41:85:41:0,85,1172 -20_10037292_10066351 7792 . T . . END=7813 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,105,1215 -20_10037292_10066351 7814 . T . . END=7814 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1167 -20_10037292_10066351 7815 . T . . END=7820 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1665 -20_10037292_10066351 7821 . T . . END=7821 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1114 -20_10037292_10066351 7822 . T . . END=7822 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 7823 . A . . END=7823 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1129 -20_10037292_10066351 7824 . C . . END=7837 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1123 -20_10037292_10066351 7838 . C . . END=7838 GT:DP:GQ:MIN_DP:PL 0/0:39:70:39:0,70,1119 -20_10037292_10066351 7839 . A . . END=7844 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1164 -20_10037292_10066351 7845 . C . . END=7846 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1123 -20_10037292_10066351 7847 . C . . END=7854 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,108,1620 -20_10037292_10066351 7855 . A . . END=7857 GT:DP:GQ:MIN_DP:PL 0/0:39:82:39:0,82,1089 -20_10037292_10066351 7858 . C . . END=7861 GT:DP:GQ:MIN_DP:PL 0/0:38:75:37:0,75,1065 -20_10037292_10066351 7862 . G . . END=7862 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1123 -20_10037292_10066351 7863 . G . . END=7865 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1124 -20_10037292_10066351 7866 . T . . END=7866 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1129 -20_10037292_10066351 7867 . A . . END=7884 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,101,1090 -20_10037292_10066351 7885 . G . . END=7885 GT:DP:GQ:MIN_DP:PL 0/0:41:94:41:0,94,1227 -20_10037292_10066351 7886 . G . . END=7897 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,110,1179 -20_10037292_10066351 7898 . T . . END=7898 GT:DP:GQ:MIN_DP:PL 0/0:41:59:41:0,59,1084 -20_10037292_10066351 7899 . A . . END=7913 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1236 -20_10037292_10066351 7914 . T . . END=7914 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 7915 . T . . END=7915 GT:DP:GQ:MIN_DP:PL 0/0:39:82:39:0,82,1146 -20_10037292_10066351 7916 . A . . END=7927 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1485 -20_10037292_10066351 7928 . C . . END=7928 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1114 -20_10037292_10066351 7929 . A . . END=7930 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 7931 . A . . END=7934 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 7935 . G . . END=7935 GT:DP:GQ:MIN_DP:PL 0/0:37:75:37:0,75,1128 -20_10037292_10066351 7936 . G . . END=7941 GT:DP:GQ:MIN_DP:PL 0/0:38:90:35:0,90,1350 -20_10037292_10066351 7942 . T . . END=7942 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,979 -20_10037292_10066351 7943 . T . . END=7945 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 7946 . C . . END=7946 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 7947 . A . . END=7948 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 7949 . T . . END=7956 GT:DP:GQ:MIN_DP:PL 0/0:31:80:30:0,80,971 -20_10037292_10066351 7957 . T . . END=7957 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,897 -20_10037292_10066351 7958 . G . . END=7981 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,888 -20_10037292_10066351 7982 . A . . END=7984 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 7985 . A . . END=7985 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 7986 . G . . END=7991 GT:DP:GQ:MIN_DP:PL 0/0:30:77:29:0,77,809 -20_10037292_10066351 7992 . A . . END=8000 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8001 . G . . END=8009 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,855 -20_10037292_10066351 8010 . G . . END=8021 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 8022 . T . . END=8022 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,890 -20_10037292_10066351 8023 . T . . END=8023 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8024 . G . . END=8024 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,900 -20_10037292_10066351 8025 . A . . END=8026 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 8027 . T . . END=8027 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,870 -20_10037292_10066351 8028 . A . . END=8034 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 8035 . G . . END=8037 GT:DP:GQ:MIN_DP:PL 0/0:28:73:28:0,73,921 -20_10037292_10066351 8038 . G . . END=8038 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8039 . C . . END=8039 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,822 -20_10037292_10066351 8040 . A . . END=8041 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8042 . T . . END=8042 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,842 -20_10037292_10066351 8043 . T . . END=8045 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8046 . C . . END=8046 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,780 -20_10037292_10066351 8047 . A . . END=8047 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8048 . G . . END=8050 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8051 . C . . END=8051 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,745 -20_10037292_10066351 8052 . A . . END=8054 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 8055 . C . . END=8055 GT:DP:GQ:MIN_DP:PL 0/0:29:63:29:0,63,853 -20_10037292_10066351 8056 . C . . END=8056 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,837 -20_10037292_10066351 8057 . C . . END=8057 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8058 . A . . END=8059 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,844 -20_10037292_10066351 8060 . T . . END=8060 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 8061 . C . . END=8061 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20_10037292_10066351 8062 . C . . END=8062 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,798 -20_10037292_10066351 8063 . A . . END=8073 GT:DP:GQ:MIN_DP:PL 0/0:30:71:27:0,71,849 -20_10037292_10066351 8074 . T . . END=8074 GT:DP:GQ:MIN_DP:PL 0/0:25:43:25:0,43,699 -20_10037292_10066351 8075 . A . . END=8075 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,812 -20_10037292_10066351 8076 . A . . END=8076 GT:DP:GQ:MIN_DP:PL 0/0:26:47:26:0,47,685 -20_10037292_10066351 8077 . A . . END=8077 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8078 . A . . END=8078 GT:DP:GQ:MIN_DP:PL 0/0:26:66:26:0,66,773 -20_10037292_10066351 8079 . G . . END=8079 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8080 . C . . END=8080 GT:DP:GQ:MIN_DP:PL 0/0:26:31:26:0,31,667 -20_10037292_10066351 8081 . A . . END=8081 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8082 . A . . END=8082 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8083 . T . . END=8083 GT:DP:GQ:MIN_DP:PL 0/0:28:37:28:0,37,743 -20_10037292_10066351 8084 . G . . END=8084 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8085 . T . . END=8085 GT:DP:GQ:MIN_DP:PL 0/0:28:25:28:0,25,743 -20_10037292_10066351 8086 . G . . END=8086 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,783 -20_10037292_10066351 8087 . A . . END=8087 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,773 -20_10037292_10066351 8088 . C . . END=8088 GT:DP:GQ:MIN_DP:PL 0/0:28:25:28:0,25,675 -20_10037292_10066351 8089 . A . . END=8089 GT:DP:GQ:MIN_DP:PL 0/0:28:50:28:0,50,799 -20_10037292_10066351 8090 . A . . END=8090 GT:DP:GQ:MIN_DP:PL 0/0:28:64:28:0,64,842 -20_10037292_10066351 8091 . G . . END=8091 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8092 . A . . END=8092 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8093 . A . . END=8093 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8094 . A . . END=8095 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,881 -20_10037292_10066351 8096 . A . . END=8098 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 8099 . T . . END=8099 GT:DP:GQ:MIN_DP:PL 0/0:29:58:29:0,58,810 -20_10037292_10066351 8100 . A . . END=8101 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8102 . A . . END=8105 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,888 -20_10037292_10066351 8106 . T . . END=8106 GT:DP:GQ:MIN_DP:PL 0/0:28:50:28:0,50,808 -20_10037292_10066351 8107 . G . . END=8107 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,829 -20_10037292_10066351 8108 . G . . END=8108 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8109 . T . . END=8110 GT:DP:GQ:MIN_DP:PL 0/0:28:64:27:0,64,791 -20_10037292_10066351 8111 . A . . END=8111 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8112 . G . . END=8112 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,816 -20_10037292_10066351 8113 . G . . END=8113 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8114 . G . . END=8114 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,659 -20_10037292_10066351 8115 . A . . END=8115 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 8116 . A . . END=8116 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,663 -20_10037292_10066351 8117 . A . . END=8117 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8118 . A . . END=8118 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,791 -20_10037292_10066351 8119 . G . . END=8119 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,801 -20_10037292_10066351 8120 . A . . END=8120 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 8121 . G . . END=8121 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,817 -20_10037292_10066351 8122 . G . . END=8122 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8123 . C . . END=8123 GT:DP:GQ:MIN_DP:PL 0/0:27:52:27:0,52,788 -20_10037292_10066351 8124 . C . . END=8125 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,1035 -20_10037292_10066351 8126 . A . . END=8126 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8127 . A . . END=8128 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,1035 -20_10037292_10066351 8129 . C . . END=8129 GT:DP:GQ:MIN_DP:PL 0/0:27:54:27:0,54,786 -20_10037292_10066351 8130 . C . . END=8130 GT:DP:GQ:MIN_DP:PL 0/0:27:33:27:0,33,742 -20_10037292_10066351 8131 . A . . END=8133 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 8134 . T . . END=8134 GT:DP:GQ:MIN_DP:PL 0/0:25:44:25:0,44,709 -20_10037292_10066351 8135 . C . . END=8135 GT:DP:GQ:MIN_DP:PL 0/0:26:47:26:0,47,776 -20_10037292_10066351 8136 . C . . END=8136 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8137 . T . . END=8137 GT:DP:GQ:MIN_DP:PL 0/0:26:33:26:0,33,726 -20_10037292_10066351 8138 . G . . END=8138 GT:DP:GQ:MIN_DP:PL 0/0:25:48:25:0,48,757 -20_10037292_10066351 8139 . G . . END=8139 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,789 -20_10037292_10066351 8140 . A . . END=8141 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8142 . A . . END=8142 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,835 -20_10037292_10066351 8143 . G . . END=8143 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 8144 . A . . END=8144 GT:DP:GQ:MIN_DP:PL 0/0:28:51:28:0,51,816 -20_10037292_10066351 8145 . T . . END=8145 GT:DP:GQ:MIN_DP:PL 0/0:28:61:28:0,61,806 -20_10037292_10066351 8146 . T . . END=8146 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 8147 . T . . END=8147 GT:DP:GQ:MIN_DP:PL 0/0:28:47:28:0,47,801 -20_10037292_10066351 8148 . G . . END=8149 GT:DP:GQ:MIN_DP:PL 0/0:29:75:28:0,75,871 -20_10037292_10066351 8150 . A . . END=8151 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,887 -20_10037292_10066351 8152 . G . . END=8153 GT:DP:GQ:MIN_DP:PL 0/0:30:64:30:0,64,889 -20_10037292_10066351 8154 . C . . END=8154 GT:DP:GQ:MIN_DP:PL 0/0:29:58:29:0,58,820 -20_10037292_10066351 8155 . A . . END=8155 GT:DP:GQ:MIN_DP:PL 0/0:28:54:28:0,54,826 -20_10037292_10066351 8156 . A . . END=8156 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8157 . C . . END=8157 GT:DP:GQ:MIN_DP:PL 0/0:28:54:28:0,54,782 -20_10037292_10066351 8158 . C . . END=8158 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,836 -20_10037292_10066351 8159 . A . . END=8159 GT:DP:GQ:MIN_DP:PL 0/0:27:56:27:0,56,768 -20_10037292_10066351 8160 . T . . END=8160 GT:DP:GQ:MIN_DP:PL 0/0:27:49:27:0,49,780 -20_10037292_10066351 8161 . A . . END=8161 GT:DP:GQ:MIN_DP:PL 0/0:27:48:27:0,48,760 -20_10037292_10066351 8162 . T . . END=8163 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8164 . G . . END=8164 GT:DP:GQ:MIN_DP:PL 0/0:28:66:28:0,66,833 -20_10037292_10066351 8165 . A . . END=8165 GT:DP:GQ:MIN_DP:PL 0/0:28:50:28:0,50,793 -20_10037292_10066351 8166 . T . . END=8167 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,852 -20_10037292_10066351 8168 . T . . END=8168 GT:DP:GQ:MIN_DP:PL 0/0:26:40:26:0,40,718 -20_10037292_10066351 8169 . G . . END=8169 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8170 . G . . END=8170 GT:DP:GQ:MIN_DP:PL 0/0:27:43:27:0,43,761 -20_10037292_10066351 8171 . A . . END=8171 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,744 -20_10037292_10066351 8172 . A . . END=8172 GT:DP:GQ:MIN_DP:PL 0/0:28:9:28:0,9,692 -20_10037292_10066351 8173 . A . . END=8173 GT:DP:GQ:MIN_DP:PL 0/0:28:57:28:0,57,856 -20_10037292_10066351 8174 . G . . END=8174 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,870 -20_10037292_10066351 8175 . T . . END=8175 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,885 -20_10037292_10066351 8176 . G . . END=8176 GT:DP:GQ:MIN_DP:PL 0/0:30:32:30:0,32,810 -20_10037292_10066351 8177 . A . . END=8177 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8178 . T . . END=8178 GT:DP:GQ:MIN_DP:PL 0/0:33:38:33:0,38,893 -20_10037292_10066351 8179 . G . . END=8179 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,895 -20_10037292_10066351 8180 . G . . END=8180 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,931 -20_10037292_10066351 8181 . A . . END=8181 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,985 -20_10037292_10066351 8182 . T . . END=8182 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1018 -20_10037292_10066351 8183 . T . . END=8183 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,940 -20_10037292_10066351 8184 . T . . END=8184 GT:DP:GQ:MIN_DP:PL 0/0:33:19:33:0,19,807 -20_10037292_10066351 8185 . C . . END=8185 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,934 -20_10037292_10066351 8186 . C . . END=8186 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,993 -20_10037292_10066351 8187 . A . . END=8188 GT:DP:GQ:MIN_DP:PL 0/0:34:64:34:0,64,982 -20_10037292_10066351 8189 . T . . END=8189 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1063 -20_10037292_10066351 8190 . T . . END=8190 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1158 -20_10037292_10066351 8191 . G . . END=8191 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1114 -20_10037292_10066351 8192 . A . . END=8192 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1115 -20_10037292_10066351 8193 . T . . END=8193 GT:DP:GQ:MIN_DP:PL 0/0:38:52:38:0,52,1041 -20_10037292_10066351 8194 . T . . END=8194 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 8195 . C . . END=8195 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1156 -20_10037292_10066351 8196 . T . . END=8196 GT:DP:GQ:MIN_DP:PL 0/0:38:66:38:0,66,1142 -20_10037292_10066351 8197 . G . . END=8197 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1113 -20_10037292_10066351 8198 . C . . END=8198 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1170 -20_10037292_10066351 8199 . T . . END=8200 GT:DP:GQ:MIN_DP:PL 0/0:38:73:38:0,73,1056 -20_10037292_10066351 8201 . A . . END=8204 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1009 -20_10037292_10066351 8205 . G . . END=8205 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,992 -20_10037292_10066351 8206 . T . . END=8206 GT:DP:GQ:MIN_DP:PL 0/0:38:36:38:0,36,1047 -20_10037292_10066351 8207 . C . . END=8207 GT:DP:GQ:MIN_DP:PL 0/0:39:85:39:0,85,1120 -20_10037292_10066351 8208 . C . . END=8208 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1126 -20_10037292_10066351 8209 . C . . END=8209 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1117 -20_10037292_10066351 8210 . T . . END=8210 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1226 -20_10037292_10066351 8211 . T . . END=8211 GT:DP:GQ:MIN_DP:PL 0/0:39:83:39:0,83,1161 -20_10037292_10066351 8212 . G . . END=8228 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,100,1138 -20_10037292_10066351 8229 . G . . END=8229 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1080 -20_10037292_10066351 8230 . A . . END=8233 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1530 -20_10037292_10066351 8234 . T . . END=8234 GT:DP:GQ:MIN_DP:PL 0/0:36:60:36:0,60,1038 -20_10037292_10066351 8235 . A . . END=8235 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1158 -20_10037292_10066351 8236 . G . . END=8236 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8237 . C . . END=8237 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1069 -20_10037292_10066351 8238 . A . . END=8243 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8244 . A . . END=8244 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1065 -20_10037292_10066351 8245 . C . . END=8249 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1022 -20_10037292_10066351 8250 . T . . END=8250 GT:DP:GQ:MIN_DP:PL 0/0:33:88:33:0,88,999 -20_10037292_10066351 8251 . C . . END=8251 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,993 -20_10037292_10066351 8252 . C . . END=8256 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1012 -20_10037292_10066351 8257 . G . . END=8257 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1098 -20_10037292_10066351 8258 . C . . END=8259 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 8260 . T . . END=8260 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1112 -20_10037292_10066351 8261 . C . . END=8261 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1185 -20_10037292_10066351 8262 . T . . END=8268 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,102,1530 -20_10037292_10066351 8269 . C . . END=8269 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1123 -20_10037292_10066351 8270 . C . . END=8272 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 8273 . T . . END=8273 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1171 -20_10037292_10066351 8274 . G . . END=8276 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 8277 . G . . END=8277 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1134 -20_10037292_10066351 8278 . C . . END=8279 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 8280 . A . . END=8281 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1159 -20_10037292_10066351 8282 . G . . END=8283 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1186 -20_10037292_10066351 8284 . T . . END=8284 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,1228 -20_10037292_10066351 8285 . T . . END=8285 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1148 -20_10037292_10066351 8286 . T . . END=8294 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 8295 . G . . END=8295 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1093 -20_10037292_10066351 8296 . G . . END=8297 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,101,1115 -20_10037292_10066351 8298 . C . . END=8298 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1125 -20_10037292_10066351 8299 . T . . END=8299 GT:DP:GQ:MIN_DP:PL 0/0:38:49:38:0,49,1079 -20_10037292_10066351 8300 . C . . END=8300 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,111,1665 -20_10037292_10066351 8301 . T . . END=8302 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1122 -20_10037292_10066351 8303 . A . . END=8304 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 8305 . C . . END=8305 GT:DP:GQ:MIN_DP:PL 0/0:39:67:39:0,67,1110 -20_10037292_10066351 8306 . A . . END=8306 GT:DP:GQ:MIN_DP:PL 0/0:39:75:39:0,75,1116 -20_10037292_10066351 8307 . C . . END=8307 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,103,1201 -20_10037292_10066351 8308 . C . . END=8308 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1183 -20_10037292_10066351 8309 . A . . END=8309 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 8310 . G . . END=8310 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1182 -20_10037292_10066351 8311 . C . . END=8317 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,100,1175 -20_10037292_10066351 8318 . T . . END=8318 GT:DP:GQ:MIN_DP:PL 0/0:42:94:42:0,94,1226 -20_10037292_10066351 8319 . A . . END=8325 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 8326 . G . . END=8326 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1124 -20_10037292_10066351 8327 . A . . END=8328 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8329 . T . . END=8335 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 8336 . G . . END=8336 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1092 -20_10037292_10066351 8337 . A . . END=8338 GT:DP:GQ:MIN_DP:PL 0/0:38:96:37:0,96,1122 -20_10037292_10066351 8339 . T . . END=8339 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1114 -20_10037292_10066351 8340 . T . . END=8343 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8344 . A . . END=8345 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,982 -20_10037292_10066351 8346 . A . . END=8349 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1011 -20_10037292_10066351 8350 . G C, 348.64 . BaseQRankSum=-1.608;DP=31;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=111600,31;ReadPosRankSum=-0.187 GT:AD:DP:GQ:PL:SB 0/1:16,14,0:30:99:356,0,430,405,472,877:9,7,5,9 -20_10037292_10066351 8351 . A . . END=8352 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1003 -20_10037292_10066351 8353 . T . . END=8353 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8354 . T . . END=8354 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,889 -20_10037292_10066351 8355 . C . . END=8357 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8358 . A . . END=8358 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,958 -20_10037292_10066351 8359 . A . . END=8360 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 8361 . A . . END=8361 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,1111 -20_10037292_10066351 8362 . C . . END=8363 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1208 -20_10037292_10066351 8364 . G . . END=8365 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1092 -20_10037292_10066351 8366 . A . . END=8366 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1109 -20_10037292_10066351 8367 . T . . END=8367 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1118 -20_10037292_10066351 8368 . T . . END=8373 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1084 -20_10037292_10066351 8374 . G . . END=8374 GT:DP:GQ:MIN_DP:PL 0/0:39:74:39:0,74,1095 -20_10037292_10066351 8375 . G . . END=8375 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1205 -20_10037292_10066351 8376 . G . . END=8376 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 8377 . T . . END=8377 GT:DP:GQ:MIN_DP:PL 0/0:39:89:39:0,89,1104 -20_10037292_10066351 8378 . G . . END=8378 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 8379 . G . . END=8379 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1095 -20_10037292_10066351 8380 . A . . END=8391 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,107,1152 -20_10037292_10066351 8392 . T . . END=8392 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1195 -20_10037292_10066351 8393 . G . . END=8411 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1139 -20_10037292_10066351 8412 . T . . END=8414 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 8415 . A . . END=8426 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 8427 . T . . END=8427 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,973 -20_10037292_10066351 8428 . C . . END=8431 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8432 . C . . END=8432 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1129 -20_10037292_10066351 8433 . T . . END=8435 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1159 -20_10037292_10066351 8436 . C . . END=8436 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1097 -20_10037292_10066351 8437 . T . . END=8446 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1530 -20_10037292_10066351 8447 . T . . END=8447 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1078 -20_10037292_10066351 8448 . C . . END=8449 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 8450 . C . . END=8450 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1098 -20_10037292_10066351 8451 . A . . END=8454 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8455 . T . . END=8458 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 8459 . G . . END=8459 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1035 -20_10037292_10066351 8460 . C . . END=8468 GT:DP:GQ:MIN_DP:PL 0/0:35:93:32:0,93,1018 -20_10037292_10066351 8469 . T . . END=8469 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8470 . C . . END=8472 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1098 -20_10037292_10066351 8473 . T . . END=8475 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 8476 . A . . END=8476 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1027 -20_10037292_10066351 8477 . C . . END=8479 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1039 -20_10037292_10066351 8480 . G . . END=8482 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8483 . T . . END=8484 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1037 -20_10037292_10066351 8485 . T . . END=8485 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8486 . A . . END=8491 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8492 . T . . END=8492 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1010 -20_10037292_10066351 8493 . G . . END=8495 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8496 . A . . END=8497 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,996 -20_10037292_10066351 8498 . C . . END=8498 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,962 -20_10037292_10066351 8499 . T . . END=8499 GT:DP:GQ:MIN_DP:PL 0/0:32:58:32:0,58,904 -20_10037292_10066351 8500 . C . . END=8500 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,901 -20_10037292_10066351 8501 . C . . END=8503 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8504 . C . . END=8508 GT:DP:GQ:MIN_DP:PL 0/0:34:81:32:0,81,1215 -20_10037292_10066351 8509 . G . . END=8511 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,936 -20_10037292_10066351 8512 . A . . END=8513 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8514 . A . . END=8514 GT:DP:GQ:MIN_DP:PL 0/0:30:62:30:0,62,808 -20_10037292_10066351 8515 . A . . END=8519 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 8520 . G . . END=8520 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,913 -20_10037292_10066351 8521 . C . . END=8521 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 8522 . A . . END=8529 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1014 -20_10037292_10066351 8530 . C . . END=8530 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,1017 -20_10037292_10066351 8531 . C . . END=8531 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1077 -20_10037292_10066351 8532 . A . . END=8532 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1093 -20_10037292_10066351 8533 . C . . END=8536 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,111,1179 -20_10037292_10066351 8537 . A . . END=8537 GT:DP:GQ:MIN_DP:PL 0/0:40:94:40:0,94,1186 -20_10037292_10066351 8538 . A . . END=8542 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,102,1184 -20_10037292_10066351 8543 . C . . END=8543 GT:DP:GQ:MIN_DP:PL 0/0:42:76:42:0,76,1186 -20_10037292_10066351 8544 . A . . END=8576 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1160 -20_10037292_10066351 8577 . G . . END=8577 GT:DP:GQ:MIN_DP:PL 0/0:38:95:38:0,95,1108 -20_10037292_10066351 8578 . T . . END=8582 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 8583 . T . . END=8583 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1108 -20_10037292_10066351 8584 . T . . END=8584 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 8585 . T . . END=8585 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1034 -20_10037292_10066351 8586 . C . . END=8588 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1041 -20_10037292_10066351 8589 . A . . END=8597 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,100,1141 -20_10037292_10066351 8598 . T . . END=8598 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1217 -20_10037292_10066351 8599 . G . . END=8644 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,99,1152 -20_10037292_10066351 8645 . T . . END=8645 GT:DP:GQ:MIN_DP:PL 0/0:44:97:44:0,97,1160 -20_10037292_10066351 8646 . C . . END=8670 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,106,1261 -20_10037292_10066351 8671 . A . . END=8671 GT:DP:GQ:MIN_DP:PL 0/0:46:94:46:0,94,1264 -20_10037292_10066351 8672 . C . . END=8710 GT:DP:GQ:MIN_DP:PL 0/0:45:99:41:0,102,1234 -20_10037292_10066351 8711 . C . . END=8711 GT:DP:GQ:MIN_DP:PL 0/0:45:98:45:0,98,1210 -20_10037292_10066351 8712 . C . . END=8719 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,120,1800 -20_10037292_10066351 8720 . C . . END=8720 GT:DP:GQ:MIN_DP:PL 0/0:47:95:47:0,95,1205 -20_10037292_10066351 8721 . A . . END=8758 GT:DP:GQ:MIN_DP:PL 0/0:50:99:47:0,101,1253 -20_10037292_10066351 8759 . C . . END=8759 GT:DP:GQ:MIN_DP:PL 0/0:51:98:51:0,98,1318 -20_10037292_10066351 8760 . T . . END=8772 GT:DP:GQ:MIN_DP:PL 0/0:50:99:48:0,112,1331 -20_10037292_10066351 8773 . G . . END=8773 GT:DP:GQ:MIN_DP:PL 0/0:47:90:47:0,90,1345 -20_10037292_10066351 8774 . G . . END=8798 GT:DP:GQ:MIN_DP:PL 0/0:47:99:46:0,100,1267 -20_10037292_10066351 8799 . T . . END=8799 GT:DP:GQ:MIN_DP:PL 0/0:46:91:46:0,91,1314 -20_10037292_10066351 8800 . C . . END=8816 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,107,1273 -20_10037292_10066351 8817 . T . . END=8817 GT:DP:GQ:MIN_DP:PL 0/0:43:9:43:0,9,868 -20_10037292_10066351 8818 . T . . END=8818 GT:DP:GQ:MIN_DP:PL 0/0:43:69:43:0,69,1016 -20_10037292_10066351 8819 . A . . END=8823 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,103,1274 -20_10037292_10066351 8824 . T . . END=8824 GT:DP:GQ:MIN_DP:PL 0/0:41:43:41:0,43,1059 -20_10037292_10066351 8825 . G . . END=8825 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,114,1710 -20_10037292_10066351 8826 . C . . END=8826 GT:DP:GQ:MIN_DP:PL 0/0:42:80:42:0,80,1084 -20_10037292_10066351 8827 . T . . END=8827 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1150 -20_10037292_10066351 8828 . G . . END=8834 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,105,1575 -20_10037292_10066351 8835 . C . . END=8835 GT:DP:GQ:MIN_DP:PL 0/0:43:66:43:0,66,1018 -20_10037292_10066351 8836 . A . . END=8845 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1238 -20_10037292_10066351 8846 . G . . END=8846 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1131 -20_10037292_10066351 8847 . G . . END=8852 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1077 -20_10037292_10066351 8853 . G . . END=8853 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1079 -20_10037292_10066351 8854 . A . . END=8859 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1103 -20_10037292_10066351 8860 . A . . END=8862 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 8863 . G . . END=8863 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,988 -20_10037292_10066351 8864 . G . . END=8864 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,955 -20_10037292_10066351 8865 . G . . END=8865 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1170 -20_10037292_10066351 8866 . A . . END=8866 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1215 -20_10037292_10066351 8867 . A . . END=8870 GT:DP:GQ:MIN_DP:PL 0/0:37:70:35:0,70,1040 -20_10037292_10066351 8871 . G . . END=8871 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,952 -20_10037292_10066351 8872 . A . . END=8872 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1019 -20_10037292_10066351 8873 . A . . END=8873 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 8874 . A . . END=8875 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1009 -20_10037292_10066351 8876 . A . . END=8876 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1170 -20_10037292_10066351 8877 . A . . END=8878 GT:DP:GQ:MIN_DP:PL 0/0:35:81:34:0,81,944 -20_10037292_10066351 8879 . A . . END=8880 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 8881 . A . . END=8882 GT:DP:GQ:MIN_DP:PL 0/0:34:81:34:0,81,1215 -20_10037292_10066351 8883 . A . . END=8883 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,1170 -20_10037292_10066351 8884 . G . . END=8884 GT:DP:GQ:MIN_DP:PL 0/0:28:0:28:0,0,701 -20_10037292_10066351 8885 . A . . END=8885 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,929 -20_10037292_10066351 8886 . AAGAAAGAAAG A, 790.03 . DP=25;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=90000,25 GT:AD:DP:GQ:PL:SB 1/1:0,18,0:18:55:804,55,0,804,55,804:0,0,15,3 -20_10037292_10066351 8897 . A . . END=8897 GT:DP:GQ:MIN_DP:PL 0/0:33:29:33:0,29,882 -20_10037292_10066351 8898 . G . . END=8898 GT:DP:GQ:MIN_DP:PL 0/0:30:0:30:0,0,664 -20_10037292_10066351 8899 . A . . END=8899 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,870 -20_10037292_10066351 8900 . A . . END=8900 GT:DP:GQ:MIN_DP:PL 0/0:29:53:29:0,53,859 -20_10037292_10066351 8901 . A . . END=8901 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 8902 . G . . END=8902 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,742 -20_10037292_10066351 8903 . A . . END=8903 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,1080 -20_10037292_10066351 8904 . A . . END=8904 GT:DP:GQ:MIN_DP:PL 0/0:30:0:30:0,0,653 -20_10037292_10066351 8905 . A . . END=8905 GT:DP:GQ:MIN_DP:PL 0/0:30:55:30:0,55,917 -20_10037292_10066351 8906 . G . . END=8906 GT:DP:GQ:MIN_DP:PL 0/0:30:0:30:0,0,592 -20_10037292_10066351 8907 . A . . END=8907 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8908 . G . . END=8908 GT:DP:GQ:MIN_DP:PL 0/0:29:56:29:0,56,775 -20_10037292_10066351 8909 . A . . END=8911 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 8912 . G . . END=8912 GT:DP:GQ:MIN_DP:PL 0/0:31:45:31:0,45,778 -20_10037292_10066351 8913 . A . . END=8913 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8914 . G . . END=8914 GT:DP:GQ:MIN_DP:PL 0/0:32:39:32:0,39,789 -20_10037292_10066351 8915 . A . . END=8915 GT:DP:GQ:MIN_DP:PL 0/0:32:55:32:0,55,861 -20_10037292_10066351 8916 . A . . END=8916 GT:DP:GQ:MIN_DP:PL 0/0:33:73:33:0,73,936 -20_10037292_10066351 8917 . A . . END=8917 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8918 . G . . END=8918 GT:DP:GQ:MIN_DP:PL 0/0:32:41:32:0,41,862 -20_10037292_10066351 8919 . A . . END=8919 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,852 -20_10037292_10066351 8920 . A . . END=8921 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8922 . G . . END=8922 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,813 -20_10037292_10066351 8923 . A . . END=8923 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8924 . G . . END=8924 GT:DP:GQ:MIN_DP:PL 0/0:32:24:32:0,24,782 -20_10037292_10066351 8925 . G . . END=8925 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,854 -20_10037292_10066351 8926 . A . . END=8927 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8928 . A . . END=8928 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,978 -20_10037292_10066351 8929 . G . . END=8929 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,916 -20_10037292_10066351 8930 . A . . END=8930 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,971 -20_10037292_10066351 8931 . G . . END=8931 GT:DP:GQ:MIN_DP:PL 0/0:34:55:34:0,55,861 -20_10037292_10066351 8932 . A . . END=8932 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 8933 . G . . END=8933 GT:DP:GQ:MIN_DP:PL 0/0:34:55:34:0,55,871 -20_10037292_10066351 8934 . A . . END=8934 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8935 . A . . END=8935 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,929 -20_10037292_10066351 8936 . A . . END=8936 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8937 . G . . END=8937 GT:DP:GQ:MIN_DP:PL 0/0:34:41:34:0,41,873 -20_10037292_10066351 8938 . A . . END=8942 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8943 . G . . END=8943 GT:DP:GQ:MIN_DP:PL 0/0:34:56:34:0,56,859 -20_10037292_10066351 8944 . A . . END=8944 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 8945 . G . . END=8945 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,999 -20_10037292_10066351 8946 . A . . END=8947 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8948 . G . . END=8948 GT:DP:GQ:MIN_DP:PL 0/0:35:70:35:0,70,915 -20_10037292_10066351 8949 . G . . END=8949 GT:DP:GQ:MIN_DP:PL 0/0:35:57:35:0,57,843 -20_10037292_10066351 8950 . A . . END=8950 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 8951 . A . . END=8951 GT:DP:GQ:MIN_DP:PL 0/0:33:77:33:0,77,925 -20_10037292_10066351 8952 . A . . END=8952 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 8953 . G . . END=8953 GT:DP:GQ:MIN_DP:PL 0/0:33:59:33:0,59,854 -20_10037292_10066351 8954 . A . . END=8954 GT:DP:GQ:MIN_DP:PL 0/0:34:83:34:0,83,996 -20_10037292_10066351 8955 . G . . END=8955 GT:DP:GQ:MIN_DP:PL 0/0:34:65:34:0,65,855 -20_10037292_10066351 8956 . A . . END=8958 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8959 . G . . END=8959 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,870 -20_10037292_10066351 8960 . A . . END=8963 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,893 -20_10037292_10066351 8964 . A . . END=8964 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8965 . G . . END=8965 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,921 -20_10037292_10066351 8966 . A . . END=8966 GT:DP:GQ:MIN_DP:PL 0/0:33:79:33:0,79,885 -20_10037292_10066351 8967 . A . . END=8967 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8968 . G . . END=8969 GT:DP:GQ:MIN_DP:PL 0/0:31:75:30:0,75,807 -20_10037292_10066351 8970 . A . . END=8975 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 8976 . A . . END=8977 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,807 -20_10037292_10066351 8978 . A . . END=8983 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,904 -20_10037292_10066351 8984 . A . . END=8986 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 8987 . G . . END=8987 GT:DP:GQ:MIN_DP:PL 0/0:32:65:32:0,65,811 -20_10037292_10066351 8988 . A . . END=8988 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,954 -20_10037292_10066351 8989 . G . . END=8989 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,832 -20_10037292_10066351 8990 . A . . END=8992 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8993 . G . . END=8994 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8995 . G . . END=8995 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,964 -20_10037292_10066351 8996 . A . . END=8996 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8997 . G . . END=8998 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,927 -20_10037292_10066351 8999 . G . . END=8999 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,935 -20_10037292_10066351 9000 . A . . END=9001 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9002 . A . . END=9011 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1019 -20_10037292_10066351 9012 . G . . END=9012 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 9013 . A . . END=9013 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 9014 . A . . END=9014 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1063 -20_10037292_10066351 9015 . G . . END=9018 GT:DP:GQ:MIN_DP:PL 0/0:38:90:37:0,90,991 -20_10037292_10066351 9019 . G . . END=9019 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,933 -20_10037292_10066351 9020 . A . . END=9022 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1066 -20_10037292_10066351 9023 . A . . END=9023 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,965 -20_10037292_10066351 9024 . A . . END=9024 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9025 . T . . END=9025 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,801 -20_10037292_10066351 9026 . G . . END=9030 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,105,1575 -20_10037292_10066351 9031 . G . . END=9031 GT:DP:GQ:MIN_DP:PL 0/0:39:66:39:0,66,992 -20_10037292_10066351 9032 . A . . END=9032 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 9033 . G . . END=9033 GT:DP:GQ:MIN_DP:PL 0/0:40:59:40:0,59,1001 -20_10037292_10066351 9034 . G . . END=9034 GT:DP:GQ:MIN_DP:PL 0/0:40:55:40:0,55,938 -20_10037292_10066351 9035 . A . . END=9036 GT:DP:GQ:MIN_DP:PL 0/0:40:84:39:0,84,1028 -20_10037292_10066351 9037 . G . . END=9037 GT:DP:GQ:MIN_DP:PL 0/0:38:13:38:0,13,819 -20_10037292_10066351 9038 . G . . END=9038 GT:DP:GQ:MIN_DP:PL 0/0:36:66:36:0,66,886 -20_10037292_10066351 9039 . A . . END=9044 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,101,1102 -20_10037292_10066351 9045 . G . . END=9045 GT:DP:GQ:MIN_DP:PL 0/0:38:80:38:0,80,1032 -20_10037292_10066351 9046 . A . . END=9046 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 9047 . G . . END=9047 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,992 -20_10037292_10066351 9048 . A . . END=9048 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9049 . C . . END=9049 GT:DP:GQ:MIN_DP:PL 0/0:35:75:35:0,75,843 -20_10037292_10066351 9050 . A . . END=9056 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 9057 . A . . END=9057 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 9058 . A . . END=9058 GT:DP:GQ:MIN_DP:PL 0/0:36:64:36:0,64,986 -20_10037292_10066351 9059 . G . . END=9060 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 9061 . A . . END=9070 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,1260 -20_10037292_10066351 9071 . A . . END=9071 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9072 . G . . END=9072 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1060 -20_10037292_10066351 9073 . A . . END=9073 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9074 . A . . END=9074 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 9075 . A . . END=9077 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1395 -20_10037292_10066351 9078 . A . . END=9079 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,986 -20_10037292_10066351 9080 . A . . END=9081 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9082 . A . . END=9082 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,984 -20_10037292_10066351 9083 . G . . END=9085 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 9086 . G . . END=9086 GT:DP:GQ:MIN_DP:PL 0/0:33:80:33:0,80,954 -20_10037292_10066351 9087 . A . . END=9087 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,899 -20_10037292_10066351 9088 . A . . END=9088 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,992 -20_10037292_10066351 9089 . G . . END=9096 GT:DP:GQ:MIN_DP:PL 0/0:35:90:32:0,90,1350 -20_10037292_10066351 9097 . A . . END=9097 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,971 -20_10037292_10066351 9098 . G . . END=9099 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9100 . A . . END=9100 GT:DP:GQ:MIN_DP:PL 0/0:33:73:33:0,73,999 -20_10037292_10066351 9101 . A . . END=9103 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 9104 . A . . END=9107 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,943 -20_10037292_10066351 9108 . A . . END=9110 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9111 . A . . END=9111 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,972 -20_10037292_10066351 9112 . A . . END=9117 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9118 . A . . END=9133 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1099 -20_10037292_10066351 9134 . A . . END=9134 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1061 -20_10037292_10066351 9135 . A . . END=9135 GT:DP:GQ:MIN_DP:PL 0/0:36:82:36:0,82,1064 -20_10037292_10066351 9136 . A . . END=9136 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9137 . C . . END=9137 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1079 -20_10037292_10066351 9138 . C . . END=9140 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9141 . A . . END=9141 GT:DP:GQ:MIN_DP:PL 0/0:37:85:37:0,85,1117 -20_10037292_10066351 9142 . A . . END=9142 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1124 -20_10037292_10066351 9143 . A . . END=9143 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9144 . A . . END=9144 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1143 -20_10037292_10066351 9145 . G . . END=9152 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1142 -20_10037292_10066351 9153 . T . . END=9153 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1295 -20_10037292_10066351 9154 . A . . END=9176 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,102,1254 -20_10037292_10066351 9177 . T . . END=9177 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1212 -20_10037292_10066351 9178 . G . . END=9180 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,107,1119 -20_10037292_10066351 9181 . G . . END=9181 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1056 -20_10037292_10066351 9182 . G . . END=9184 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1197 -20_10037292_10066351 9185 . T . . END=9185 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1152 -20_10037292_10066351 9186 . T . . END=9186 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1209 -20_10037292_10066351 9187 . T . . END=9187 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1113 -20_10037292_10066351 9188 . C . . END=9193 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,105,1208 -20_10037292_10066351 9194 . A . . END=9194 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1134 -20_10037292_10066351 9195 . C . . END=9201 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,102,1314 -20_10037292_10066351 9202 . T . . END=9202 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1233 -20_10037292_10066351 9203 . C . . END=9246 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,114,1272 -20_10037292_10066351 9247 . T . . END=9247 GT:DP:GQ:MIN_DP:PL 0/0:44:90:44:0,90,1239 -20_10037292_10066351 9248 . T . . END=9263 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,117,1755 -20_10037292_10066351 9264 . A . . END=9264 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1293 -20_10037292_10066351 9265 . A . . END=9280 GT:DP:GQ:MIN_DP:PL 0/0:44:99:41:0,106,1208 -20_10037292_10066351 9281 . T . . END=9281 GT:DP:GQ:MIN_DP:PL 0/0:45:89:45:0,89,1396 -20_10037292_10066351 9282 . G . . END=9301 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,99,1485 -20_10037292_10066351 9302 . A . . END=9306 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 9307 . A . . END=9309 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 9310 . C . . END=9314 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1141 -20_10037292_10066351 9315 . G . . END=9360 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,102,1243 -20_10037292_10066351 9361 . G . . END=9361 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1076 -20_10037292_10066351 9362 . C . . END=9369 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,105,1575 -20_10037292_10066351 9370 . A . . END=9370 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1042 -20_10037292_10066351 9371 . C . . END=9374 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 9375 . A . . END=9375 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1118 -20_10037292_10066351 9376 . C . . END=9376 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9377 . A . . END=9382 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1117 -20_10037292_10066351 9383 . C . . END=9385 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9386 . A . . END=9386 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1091 -20_10037292_10066351 9387 . T . . END=9400 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1158 -20_10037292_10066351 9401 . T . . END=9401 GT:DP:GQ:MIN_DP:PL 0/0:36:73:36:0,73,1066 -20_10037292_10066351 9402 . C . . END=9408 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1143 -20_10037292_10066351 9409 . C . . END=9409 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1193 -20_10037292_10066351 9410 . C . . END=9412 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,111,1665 -20_10037292_10066351 9413 . C . . END=9413 GT:DP:GQ:MIN_DP:PL 0/0:42:94:42:0,94,1240 -20_10037292_10066351 9414 . C . . END=9463 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,104,1316 -20_10037292_10066351 9464 . A . . END=9464 GT:DP:GQ:MIN_DP:PL 0/0:42:79:42:0,79,1237 -20_10037292_10066351 9465 . A . . END=9468 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 9469 . T . . END=9469 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1174 -20_10037292_10066351 9470 . C . . END=9478 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1485 -20_10037292_10066351 9479 . A . . END=9480 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 9481 . G . . END=9484 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 9485 . A . . END=9486 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1037 -20_10037292_10066351 9487 . C . . END=9492 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 9493 . G . . END=9493 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1162 -20_10037292_10066351 9494 . A . . END=9496 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9497 . T . . END=9497 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1105 -20_10037292_10066351 9498 . C . . END=9513 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1169 -20_10037292_10066351 9514 . C . . END=9514 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1203 -20_10037292_10066351 9515 . C . . END=9533 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,105,1101 -20_10037292_10066351 9534 . A . . END=9534 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,960 -20_10037292_10066351 9535 . A . . END=9535 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9536 . T C, 936.06 . DP=32;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=115200,32 GT:AD:DP:GQ:PL:SB 1/1:0,32,0:32:95:950,95,0,950,95,950:0,0,16,16 -20_10037292_10066351 9537 . T . . END=9537 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,993 -20_10037292_10066351 9538 . C . . END=9538 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9539 . A . . END=9540 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,974 -20_10037292_10066351 9541 . C . . END=9544 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 9545 . A . . END=9545 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1085 -20_10037292_10066351 9546 . T . . END=9546 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1088 -20_10037292_10066351 9547 . T . . END=9554 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 9555 . A . . END=9565 GT:DP:GQ:MIN_DP:PL 0/0:38:90:34:0,90,1110 -20_10037292_10066351 9566 . T . . END=9568 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 9569 . C . . END=9569 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,899 -20_10037292_10066351 9570 . T . . END=9573 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,900 -20_10037292_10066351 9574 . C . . END=9574 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 9575 . C . . END=9575 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1076 -20_10037292_10066351 9576 . T . . END=9588 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 9589 . A . . END=9589 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,952 -20_10037292_10066351 9590 . C . . END=9597 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 9598 . G . . END=9598 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,865 -20_10037292_10066351 9599 . C . . END=9600 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 9601 . G . . END=9601 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,868 -20_10037292_10066351 9602 . T . . END=9665 GT:DP:GQ:MIN_DP:PL 0/0:43:99:37:0,100,1177 -20_10037292_10066351 9666 . T . . END=9666 GT:DP:GQ:MIN_DP:PL 0/0:50:88:50:0,88,1434 -20_10037292_10066351 9667 . T . . END=9848 GT:DP:GQ:MIN_DP:PL 0/0:57:99:49:0,110,1475 -20_10037292_10066351 9849 . A . . END=9849 GT:DP:GQ:MIN_DP:PL 0/0:54:78:54:0,78,1253 -20_10037292_10066351 9850 . C . . END=9859 GT:DP:GQ:MIN_DP:PL 0/0:50:99:50:0,103,1432 -20_10037292_10066351 12912 . G . . END=12915 GT:DP:GQ:MIN_DP:PL 0/0:29:75:27:0,75,1125 -20_10037292_10066351 12916 . A . . END=12919 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 12920 . A . . END=12920 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 12921 . G . . END=12921 GT:DP:GQ:MIN_DP:PL 0/0:28:66:28:0,66,844 -20_10037292_10066351 12922 . A . . END=12927 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 -20_10037292_10066351 12928 . A . . END=12934 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 12935 . C . . END=12939 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,875 -20_10037292_10066351 12940 . A . . END=12947 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1530 -20_10037292_10066351 12948 . G . . END=12948 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,1112 -20_10037292_10066351 12949 . G . . END=12956 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 12957 . A . . END=12957 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,990 -20_10037292_10066351 12958 . A . . END=12966 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 12967 . C . . END=12976 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1350 -20_10037292_10066351 12977 . C . . END=12977 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,835 -20_10037292_10066351 12978 . A . . END=12981 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,952 -20_10037292_10066351 12982 . T . . END=12982 GT:DP:GQ:MIN_DP:PL 0/0:30:50:30:0,50,808 -20_10037292_10066351 12983 . T . . END=12986 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,886 -20_10037292_10066351 12987 . G . . END=12987 GT:DP:GQ:MIN_DP:PL 0/0:30:70:30:0,70,861 -20_10037292_10066351 12988 . A . . END=12992 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,967 -20_10037292_10066351 12993 . G . . END=12994 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 12995 . C . . END=12997 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 12998 . G . . END=12999 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 13000 . C . . END=13000 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,971 -20_10037292_10066351 13001 . C . . END=13002 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13003 . G . . END=13006 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 13007 . T . . END=13011 GT:DP:GQ:MIN_DP:PL 0/0:30:80:28:0,80,804 -20_10037292_10066351 13012 . G . . END=13012 GT:DP:GQ:MIN_DP:PL 0/0:30:61:30:0,61,937 -20_10037292_10066351 13013 . A . . END=13015 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 13016 . T . . END=13023 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,817 -20_10037292_10066351 13024 . A . . END=13024 GT:DP:GQ:MIN_DP:PL 0/0:31:82:31:0,82,915 -20_10037292_10066351 13025 . A . . END=13027 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,954 -20_10037292_10066351 13028 . G . . END=13028 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13029 . T . . END=13029 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,799 -20_10037292_10066351 13030 . A . . END=13033 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 13034 . A . . END=13034 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13035 . G . . END=13035 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13036 . T . . END=13037 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 13038 . T . . END=13038 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,969 -20_10037292_10066351 13039 . G . . END=13042 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13043 . T . . END=13043 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,992 -20_10037292_10066351 13044 . T . . END=13047 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,959 -20_10037292_10066351 13048 . T . . END=13062 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1011 -20_10037292_10066351 13063 . T . . END=13063 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1061 -20_10037292_10066351 13064 . T . . END=13064 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1049 -20_10037292_10066351 13065 . T . . END=13068 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1087 -20_10037292_10066351 13069 . C . . END=13072 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1102 -20_10037292_10066351 13073 . G . . END=13073 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 13074 . C . . END=13074 GT:DP:GQ:MIN_DP:PL 0/0:36:87:36:0,87,1305 -20_10037292_10066351 13075 . T . . END=13077 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 13078 . T . . END=13080 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 13081 . C . . END=13082 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 13083 . T . . END=13083 GT:DP:GQ:MIN_DP:PL 0/0:35:81:35:0,81,929 -20_10037292_10066351 13084 . C . . END=13084 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 13085 . T . . END=13085 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 13086 . C . . END=13088 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1395 -20_10037292_10066351 13089 . A . . END=13089 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1050 -20_10037292_10066351 13090 . A . . END=13092 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1062 -20_10037292_10066351 13093 . G . . END=13094 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 13095 . T . . END=13095 GT:DP:GQ:MIN_DP:PL 0/0:34:63:34:0,63,942 -20_10037292_10066351 13096 . T . . END=13098 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1047 -20_10037292_10066351 13099 . A . . END=13102 GT:DP:GQ:MIN_DP:PL 0/0:35:93:33:0,93,1395 -20_10037292_10066351 13103 . C . . END=13103 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1050 -20_10037292_10066351 13104 . A . . END=13104 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13105 . C . . END=13125 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1127 -20_10037292_10066351 13126 . A . . END=13126 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1081 -20_10037292_10066351 13127 . A . . END=13127 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,100,1131 -20_10037292_10066351 13128 . T . . END=13128 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1135 -20_10037292_10066351 13129 . T . . END=13159 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,107,1215 -20_10037292_10066351 13160 . T . . END=13160 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1223 -20_10037292_10066351 13161 . T . . END=13168 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,106,1237 -20_10037292_10066351 13169 . G . . END=13170 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1217 -20_10037292_10066351 13171 . C . . END=13189 GT:DP:GQ:MIN_DP:PL 0/0:46:99:43:0,99,1275 -20_10037292_10066351 13190 . A . . END=13190 GT:DP:GQ:MIN_DP:PL 0/0:45:91:45:0,91,1329 -20_10037292_10066351 13191 . G . . END=13209 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,100,1211 -20_10037292_10066351 13210 . A . . END=13210 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1107 -20_10037292_10066351 13211 . G . . END=13374 GT:DP:GQ:MIN_DP:PL 0/0:44:99:37:0,99,1159 -20_10037292_10066351 13375 . C T, 725.64 . BaseQRankSum=0.171;DP=58;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=208800,58;ReadPosRankSum=0.415 GT:AD:DP:GQ:PL:SB 0/1:28,29,0:57:99:733,0,679,816,765,1581:14,14,9,20 -20_10037292_10066351 13376 . C . . END=13438 GT:DP:GQ:MIN_DP:PL 0/0:55:99:47:0,111,1631 -20_10037292_10066351 13439 . G . . END=13439 GT:DP:GQ:MIN_DP:PL 0/0:47:90:47:0,90,1325 -20_10037292_10066351 13440 . T . . END=13455 GT:DP:GQ:MIN_DP:PL 0/0:46:99:44:0,102,1278 -20_10037292_10066351 13456 . C . . END=13456 GT:DP:GQ:MIN_DP:PL 0/0:46:94:46:0,94,1305 -20_10037292_10066351 13457 . T . . END=13487 GT:DP:GQ:MIN_DP:PL 0/0:47:99:40:0,107,1330 -20_10037292_10066351 13488 . A . . END=13488 GT:DP:GQ:MIN_DP:PL 0/0:39:72:39:0,72,1128 -20_10037292_10066351 13489 . C . . END=13489 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 13490 . A . . END=13490 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,1203 -20_10037292_10066351 13491 . G . . END=13535 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,99,1231 -20_10037292_10066351 13536 . T C, 583.64 . BaseQRankSum=1.634;DP=44;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=158400,44;ReadPosRankSum=-0.200 GT:AD:DP:GQ:PL:SB 0/1:21,23,0:44:99:591,0,526,654,594,1248:9,12,12,11 -20_10037292_10066351 13537 . T . . END=13687 GT:DP:GQ:MIN_DP:PL 0/0:49:99:38:0,103,1209 -20_10037292_10066351 13688 . A . . END=13688 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1191 -20_10037292_10066351 13689 . T . . END=13691 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 13692 . T . . END=13692 GT:DP:GQ:MIN_DP:PL 0/0:39:89:39:0,89,1224 -20_10037292_10066351 13693 . C . . END=13745 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,100,1220 -20_10037292_10066351 13746 . A . . END=13746 GT:DP:GQ:MIN_DP:PL 0/0:48:82:48:0,82,1344 -20_10037292_10066351 13747 . G . . END=13875 GT:DP:GQ:MIN_DP:PL 0/0:48:99:42:0,101,1231 -20_10037292_10066351 13876 . A . . END=13876 GT:DP:GQ:MIN_DP:PL 0/0:40:73:40:0,73,1107 -20_10037292_10066351 13877 . A . . END=13881 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,116,1281 -20_10037292_10066351 13882 . C . . END=13882 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1274 -20_10037292_10066351 13883 . C . . END=13893 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,101,1231 -20_10037292_10066351 13894 . T . . END=13894 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1440 -20_10037292_10066351 13895 . A . . END=13895 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1186 -20_10037292_10066351 13896 . A . . END=13897 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13898 . T . . END=13898 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1055 -20_10037292_10066351 13899 . T . . END=13899 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1008 -20_10037292_10066351 13900 . A . . END=13900 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13901 . T . . END=13915 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,1034 -20_10037292_10066351 13916 . T . . END=13916 GT:DP:GQ:MIN_DP:PL 0/0:42:91:42:0,91,1137 -20_10037292_10066351 13917 . A . . END=13918 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,100,1176 -20_10037292_10066351 13919 . T . . END=13919 GT:DP:GQ:MIN_DP:PL 0/0:42:94:42:0,94,1163 -20_10037292_10066351 13920 . T . . END=13941 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,103,1099 -20_10037292_10066351 13942 . T . . END=13942 GT:DP:GQ:MIN_DP:PL 0/0:42:95:42:0,95,1134 -20_10037292_10066351 13943 . A . . END=13981 GT:DP:GQ:MIN_DP:PL 0/0:45:99:41:0,102,1152 -20_10037292_10066351 13982 . G . . END=13982 GT:DP:GQ:MIN_DP:PL 0/0:45:94:45:0,94,1300 -20_10037292_10066351 13983 . A . . END=13992 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,113,1242 -20_10037292_10066351 13993 . A . . END=13993 GT:DP:GQ:MIN_DP:PL 0/0:43:93:43:0,93,1200 -20_10037292_10066351 13994 . T . . END=14022 GT:DP:GQ:MIN_DP:PL 0/0:44:99:38:0,105,1172 -20_10037292_10066351 14023 . C . . END=14023 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1103 -20_10037292_10066351 14024 . A . . END=14037 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,102,1121 -20_10037292_10066351 14038 . G . . END=14038 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1166 -20_10037292_10066351 14039 . T . . END=14042 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,101,1109 -20_10037292_10066351 14043 . A . . END=14043 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1105 -20_10037292_10066351 14044 . A . . END=14051 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,108,1620 -20_10037292_10066351 14052 . G . . END=14063 GT:DP:GQ:MIN_DP:PL 0/0:38:96:36:0,96,1440 -20_10037292_10066351 14064 . G . . END=14064 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 14065 . T . . END=14065 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,859 -20_10037292_10066351 14066 . G . . END=14066 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 14067 . C . . END=14075 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 14076 . T . . END=14076 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,986 -20_10037292_10066351 14077 . T . . END=14079 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 14080 . A . . END=14081 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1009 -20_10037292_10066351 14082 . C . . END=14084 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 14085 . C . . END=14085 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1104 -20_10037292_10066351 14086 . C . . END=14086 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 14087 . A . . END=14097 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 14098 . G . . END=14099 GT:DP:GQ:MIN_DP:PL 0/0:33:80:32:0,80,872 -20_10037292_10066351 14100 . A . . END=14101 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1011 -20_10037292_10066351 14102 . T . . END=14102 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,929 -20_10037292_10066351 14103 . C . . END=14103 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 14104 . A . . END=14104 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,971 -20_10037292_10066351 14105 . C . . END=14107 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 14108 . A . . END=14108 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 14109 . C . . END=14109 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,995 -20_10037292_10066351 14110 . T . . END=14112 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 14113 . A . . END=14118 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1043 -20_10037292_10066351 14119 . T . . END=14119 GT:DP:GQ:MIN_DP:PL 0/0:36:85:36:0,85,1054 -20_10037292_10066351 14120 . C . . END=14123 GT:DP:GQ:MIN_DP:PL 0/0:36:93:34:0,93,1395 -20_10037292_10066351 14124 . C . . END=14124 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1014 -20_10037292_10066351 14125 . A . . END=14125 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,1057 -20_10037292_10066351 14126 . G . . END=14126 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1037 -20_10037292_10066351 14127 . C . . END=14127 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,889 -20_10037292_10066351 14128 . G . . END=14130 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,102,1006 -20_10037292_10066351 14131 . C . . END=14131 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,991 -20_10037292_10066351 14132 . G . . END=14139 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,104,1190 -20_10037292_10066351 14140 . A . . END=14140 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1163 -20_10037292_10066351 14141 . C . . END=14155 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,100,1070 -20_10037292_10066351 14156 . T C, 250.64 . BaseQRankSum=3.197;DP=38;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=136800,38;ReadPosRankSum=1.134 GT:AD:DP:GQ:PL:SB 0/1:25,11,0:36:99:258,0,676,333,709,1042:16,9,4,7 -20_10037292_10066351 14157 . T . . END=14170 GT:DP:GQ:MIN_DP:PL 0/0:44:99:40:0,105,1282 -20_10037292_10066351 14171 . A . . END=14171 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1214 -20_10037292_10066351 14172 . C . . END=14192 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,104,1294 -20_10037292_10066351 14193 . T . . END=14193 GT:DP:GQ:MIN_DP:PL 0/0:46:92:46:0,92,1310 -20_10037292_10066351 14194 . C . . END=14268 GT:DP:GQ:MIN_DP:PL 0/0:41:99:35:0,99,1065 -20_10037292_10066351 14269 . C . . END=14272 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1092 -20_10037292_10066351 14273 . A . . END=14277 GT:DP:GQ:MIN_DP:PL 0/0:36:84:35:0,84,1260 -20_10037292_10066351 14278 . A . . END=14279 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 14280 . C . . END=14324 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,1011 -20_10037292_10066351 14325 . T . . END=14331 GT:DP:GQ:MIN_DP:PL 0/0:37:92:35:0,92,1076 -20_10037292_10066351 14332 . C . . END=14332 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1040 -20_10037292_10066351 14333 . T . . END=14335 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 14336 . G . . END=14336 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1026 -20_10037292_10066351 14337 . A . . END=14338 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 14339 . G . . END=14344 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 14345 . A . . END=14348 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 14349 . T . . END=14351 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 14352 . G . . END=14352 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1064 -20_10037292_10066351 14353 . T . . END=14376 GT:DP:GQ:MIN_DP:PL 0/0:40:99:35:0,99,1159 -20_10037292_10066351 14377 . C . . END=14377 GT:DP:GQ:MIN_DP:PL 0/0:45:92:45:0,92,1330 -20_10037292_10066351 14378 . C . . END=14402 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,110,1227 -20_10037292_10066351 14403 . G A, 145.64 . BaseQRankSum=2.632;DP=42;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=151200,42;ReadPosRankSum=0.252 GT:AD:DP:GQ:PL:SB 0/1:32,9,0:41:99:153,0,821,249,848,1097:15,17,5,4 -20_10037292_10066351 14404 . T . . END=14450 GT:DP:GQ:MIN_DP:PL 0/0:43:99:37:0,99,1183 -20_10037292_10066351 14451 . T . . END=14454 GT:DP:GQ:MIN_DP:PL 0/0:38:90:37:0,90,1350 -20_10037292_10066351 14455 . G . . END=14457 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,1260 -20_10037292_10066351 14458 . A . . END=14470 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 14471 . C . . END=14471 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,957 -20_10037292_10066351 14472 . T . . END=14473 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1032 -20_10037292_10066351 14474 . A . . END=14492 GT:DP:GQ:MIN_DP:PL 0/0:38:99:33:0,99,1015 -20_10037292_10066351 14493 . A . . END=14493 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1013 -20_10037292_10066351 14494 . A . . END=14495 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 14496 . T . . END=14496 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1103 -20_10037292_10066351 14497 . A . . END=14500 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 14501 . G . . END=14502 GT:DP:GQ:MIN_DP:PL 0/0:39:83:38:0,83,1070 -20_10037292_10066351 14503 . C . . END=14513 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,99,1485 -20_10037292_10066351 14514 . A . . END=14517 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 14518 . A . . END=14519 GT:DP:GQ:MIN_DP:PL 0/0:36:87:36:0,87,1305 -20_10037292_10066351 14520 . A . . END=14523 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 14524 . T . . END=14524 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1001 -20_10037292_10066351 14525 . T . . END=14527 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 14528 . T . . END=14528 GT:DP:GQ:MIN_DP:PL 0/0:32:67:32:0,67,931 -20_10037292_10066351 14529 . T . . END=14529 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,950 -20_10037292_10066351 14530 . T . . END=14530 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 14531 . A . . END=14548 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,99,1108 -20_10037292_10066351 14549 . C . . END=14549 GT:DP:GQ:MIN_DP:PL 0/0:40:83:40:0,83,1170 -20_10037292_10066351 14550 . A . . END=14557 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1665 -20_10037292_10066351 14558 . C . . END=14558 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1130 -20_10037292_10066351 14559 . C . . END=14609 GT:DP:GQ:MIN_DP:PL 0/0:45:99:40:0,101,1298 -20_10037292_10066351 14610 . A . . END=14610 GT:DP:GQ:MIN_DP:PL 0/0:44:92:44:0,92,1272 -20_10037292_10066351 14611 . C . . END=14683 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,99,1157 -20_10037292_10066351 14684 . T . . END=14684 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14685 . T . . END=14685 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 14686 . A . . END=14692 GT:DP:GQ:MIN_DP:PL 0/0:37:92:35:0,92,1073 -20_10037292_10066351 14693 . T . . END=14693 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 14694 . G . . END=14699 GT:DP:GQ:MIN_DP:PL 0/0:36:93:34:0,93,1109 -20_10037292_10066351 14700 . A . . END=14700 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1091 -20_10037292_10066351 14701 . T . . END=14701 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 14702 . T . . END=14702 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1053 -20_10037292_10066351 14703 . A . . END=14703 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 14704 . A . . END=14708 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 14709 . G . . END=14714 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14715 . A . . END=14715 GT:DP:GQ:MIN_DP:PL 0/0:36:86:36:0,86,1081 -20_10037292_10066351 14716 . C . . END=14717 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14718 . T . . END=14721 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 14722 . A . . END=14722 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1110 -20_10037292_10066351 14723 . T . . END=14725 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 14726 . A . . END=14726 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1117 -20_10037292_10066351 14727 . T . . END=14737 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1099 diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf.idx b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf.idx deleted file mode 100644 index a641f33b6..000000000 Binary files a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf.idx and /dev/null differ diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf deleted file mode 100644 index 710aba049..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf +++ /dev/null @@ -1,1676 +0,0 @@ -##fileformat=VCFv4.2 -##ALT= -##FILTER= -##FORMAT= -##FORMAT= 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G . . END=3278 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 3279 . A . . END=3279 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1084 -20_10037292_10066351 3280 . A . . END=3281 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 3282 . T . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 3283 . T . . END=3283 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 3284 . T . . END=3284 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 3285 . T . . END=3293 GT:DP:GQ:MIN_DP:PL 0/0:35:81:31:0,81,1215 -20_10037292_10066351 3294 . A . . END=3302 GT:DP:GQ:MIN_DP:PL 0/0:33:90:30:0,90,970 -20_10037292_10066351 3303 . G . . END=3304 GT:DP:GQ:MIN_DP:PL 0/0:33:72:32:0,72,963 -20_10037292_10066351 3305 . C . . END=3309 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1053 -20_10037292_10066351 3310 . A . . END=3319 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1086 -20_10037292_10066351 3320 . A . . END=3320 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,959 -20_10037292_10066351 3321 . A . . END=3322 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 3323 . G . . END=3323 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,953 -20_10037292_10066351 3324 . T . . END=3325 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 3326 . G . . END=3326 GT:DP:GQ:MIN_DP:PL 0/0:31:60:31:0,60,873 -20_10037292_10066351 3327 . C . . END=3328 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 3329 . T . . END=3329 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 3330 . G . . END=3330 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,949 -20_10037292_10066351 3331 . T . . END=3332 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 3333 . A . . END=3335 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,892 -20_10037292_10066351 3336 . T . . END=3337 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 3338 . C . . END=3338 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,851 -20_10037292_10066351 3339 . C . . END=3339 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 3340 . T . . END=3340 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,888 -20_10037292_10066351 3341 . A . . END=3343 GT:DP:GQ:MIN_DP:PL 0/0:30:84:28:0,84,910 -20_10037292_10066351 3344 . T . . END=3344 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,832 -20_10037292_10066351 3345 . T . . END=3348 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,891 -20_10037292_10066351 3349 . A . . END=3349 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,904 -20_10037292_10066351 3350 . G . . END=3350 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,910 -20_10037292_10066351 3351 . T . . END=3352 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,975 -20_10037292_10066351 3353 . G . . END=3354 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,846 -20_10037292_10066351 3355 . A . . END=3355 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,978 -20_10037292_10066351 3356 . T . . END=3357 GT:DP:GQ:MIN_DP:PL 0/0:31:67:31:0,67,916 -20_10037292_10066351 3358 . A . . END=3363 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1017 -20_10037292_10066351 3364 . G . . END=3364 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,947 -20_10037292_10066351 3365 . A . . END=3365 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3366 . C . . END=3366 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,963 -20_10037292_10066351 3367 . T . . END=3369 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 3370 . C . . END=3370 GT:DP:GQ:MIN_DP:PL 0/0:32:46:32:0,46,903 -20_10037292_10066351 3371 . A . . END=3371 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3372 . A . . END=3372 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,905 -20_10037292_10066351 3373 . A . . END=3374 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3375 . G . . END=3375 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,922 -20_10037292_10066351 3376 . C . . END=3376 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 3377 . A . . END=3381 GT:DP:GQ:MIN_DP:PL 0/0:32:84:31:0,84,1260 -20_10037292_10066351 3382 . A . . END=3385 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3386 . A . . END=3387 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,964 -20_10037292_10066351 3388 . A . . END=3397 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 3398 . A . . END=3398 GT:DP:GQ:MIN_DP:PL 0/0:31:75:31:0,75,920 -20_10037292_10066351 3399 . T . . END=3399 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3400 . T . . END=3400 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3401 . T . . END=3402 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 3403 . T . . END=3403 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3404 . C . . END=3405 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,944 -20_10037292_10066351 3406 . G . . END=3407 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,859 -20_10037292_10066351 3408 . G . . END=3408 GT:DP:GQ:MIN_DP:PL 0/0:32:62:32:0,62,890 -20_10037292_10066351 3409 . T . . END=3418 GT:DP:GQ:MIN_DP:PL 0/0:33:81:30:0,81,1215 -20_10037292_10066351 3419 . T . . END=3419 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,827 -20_10037292_10066351 3420 . T . . END=3421 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 3422 . T . . END=3430 GT:DP:GQ:MIN_DP:PL 0/0:29:75:28:0,75,1125 -20_10037292_10066351 3431 . T . . END=3439 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 3440 . A . . END=3440 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,782 -20_10037292_10066351 3441 . T . . END=3442 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 3443 . T . . END=3443 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3444 . T . . END=3445 GT:DP:GQ:MIN_DP:PL 0/0:28:64:28:0,64,722 -20_10037292_10066351 3446 . G . . END=3446 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3447 . C . . END=3447 GT:DP:GQ:MIN_DP:PL 0/0:29:53:29:0,53,694 -20_10037292_10066351 3448 . T . . END=3449 GT:DP:GQ:MIN_DP:PL 0/0:31:76:30:0,76,827 -20_10037292_10066351 3450 . A . . END=3450 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3451 . C . . END=3452 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,715 -20_10037292_10066351 3453 . T . . END=3455 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 3456 . A . . END=3456 GT:DP:GQ:MIN_DP:PL 0/0:31:23:31:0,23,766 -20_10037292_10066351 3457 . T . . END=3460 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3461 . C . . END=3461 GT:DP:GQ:MIN_DP:PL 0/0:30:89:30:0,89,873 -20_10037292_10066351 3462 . T . . END=3462 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3463 . G . . END=3463 GT:DP:GQ:MIN_DP:PL 0/0:31:44:31:0,44,739 -20_10037292_10066351 3464 . T . . END=3468 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3469 . C . . END=3469 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,816 -20_10037292_10066351 3470 . T . . END=3470 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 3471 . T . . END=3478 GT:DP:GQ:MIN_DP:PL 0/0:32:75:32:0,75,1125 -20_10037292_10066351 3479 . T . . END=3479 GT:DP:GQ:MIN_DP:PL 0/0:34:36:34:0,36,906 -20_10037292_10066351 3480 . C CT, 503.03 . DP=23;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=82800,23 GT:AD:DP:GQ:PL:SB 1/1:0,18,0:18:54:517,54,0,517,54,517:0,0,7,11 -20_10037292_10066351 3481 . T . . END=3481 GT:DP:GQ:MIN_DP:PL 0/0:21:51:21:0,51,765 -20_10037292_10066351 3482 . T . . END=3482 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 -20_10037292_10066351 3483 . T . . END=3487 GT:DP:GQ:MIN_DP:PL 0/0:20:51:19:0,51,765 -20_10037292_10066351 3488 . T . . END=3488 GT:DP:GQ:MIN_DP:PL 0/0:19:42:19:0,42,571 -20_10037292_10066351 3489 . A . . END=3489 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,521 -20_10037292_10066351 3490 . C . . END=3490 GT:DP:GQ:MIN_DP:PL 0/0:17:35:17:0,35,431 -20_10037292_10066351 3491 . A . . END=3495 GT:DP:GQ:MIN_DP:PL 0/0:17:48:17:0,48,720 -20_10037292_10066351 3496 . A . . END=3498 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,473 -20_10037292_10066351 3499 . C . . END=3499 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,428 -20_10037292_10066351 3500 . G . . END=3500 GT:DP:GQ:MIN_DP:PL 0/0:16:31:16:0,31,379 -20_10037292_10066351 3501 . T . . END=3501 GT:DP:GQ:MIN_DP:PL 0/0:17:48:17:0,48,720 -20_10037292_10066351 3502 . A . . END=3503 GT:DP:GQ:MIN_DP:PL 0/0:19:54:18:0,54,550 -20_10037292_10066351 3504 . T . . END=3504 GT:DP:GQ:MIN_DP:PL 0/0:19:48:19:0,48,720 -20_10037292_10066351 3505 . A . . END=3506 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 -20_10037292_10066351 3507 . T . . END=3519 GT:DP:GQ:MIN_DP:PL 0/0:19:54:18:0,54,501 -20_10037292_10066351 3520 . AT A, 609.03 . DP=18;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=64800,18 GT:AD:DP:GQ:PL:SB 1/1:0,18,0:18:54:623,54,0,623,54,623:0,0,9,9 -20_10037292_10066351 3522 . T . . END=3525 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,550 -20_10037292_10066351 3526 . T . . END=3527 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,607 -20_10037292_10066351 3528 . T . . END=3528 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 -20_10037292_10066351 3529 . T A, 155.64 . BaseQRankSum=-0.544;DP=21;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=75600,21;ReadPosRankSum=-1.158 GT:AD:DP:GQ:PL:SB 0/1:12,8,0:20:99:163,0,328,199,352,551:5,7,5,3 -20_10037292_10066351 3530 . A . . END=3530 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,941 -20_10037292_10066351 3531 . A . . END=3533 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 3534 . A . . END=3534 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1170 -20_10037292_10066351 3535 . A . . END=3536 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,891 -20_10037292_10066351 3537 . A . . END=3546 GT:DP:GQ:MIN_DP:PL 0/0:29:72:26:0,72,1080 -20_10037292_10066351 3547 . A . . END=3547 GT:DP:GQ:MIN_DP:PL 0/0:26:56:26:0,56,731 -20_10037292_10066351 3548 . G . . END=3549 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 3550 . T . . END=3553 GT:DP:GQ:MIN_DP:PL 0/0:26:60:25:0,60,707 -20_10037292_10066351 3554 . A . . END=3556 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 3557 . A . . END=3557 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 3558 . A . . END=3559 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,819 -20_10037292_10066351 3560 . G . . END=3560 GT:DP:GQ:MIN_DP:PL 0/0:27:54:27:0,54,721 -20_10037292_10066351 3561 . T . . END=3562 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 3563 . C . . END=3569 GT:DP:GQ:MIN_DP:PL 0/0:29:81:27:0,81,833 -20_10037292_10066351 3570 . C . . END=3570 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 3571 . C . . END=3571 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,788 -20_10037292_10066351 3572 . A . . END=3583 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 3584 . T . . END=3594 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,1125 -20_10037292_10066351 3595 . C . . END=3595 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 3596 . T . . END=3602 GT:DP:GQ:MIN_DP:PL 0/0:27:75:25:0,75,800 -20_10037292_10066351 3603 . T . . END=3603 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,824 -20_10037292_10066351 3604 . G . . END=3611 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 3612 . G . . END=3612 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,786 -20_10037292_10066351 3613 . T . . END=3613 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 3614 . G . . END=3614 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,825 -20_10037292_10066351 3615 . C . . END=3615 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 3616 . A . . END=3616 GT:DP:GQ:MIN_DP:PL 0/0:27:61:27:0,61,752 -20_10037292_10066351 3617 . T . . END=3617 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,774 -20_10037292_10066351 3618 . T . . END=3619 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 3620 . C . . END=3620 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,813 -20_10037292_10066351 3621 . A . . END=3638 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 -20_10037292_10066351 3639 . G . . END=3639 GT:DP:GQ:MIN_DP:PL 0/0:28:67:28:0,67,821 -20_10037292_10066351 3640 . A . . END=3640 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3641 . A . . END=3645 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 3646 . G . . END=3646 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,894 -20_10037292_10066351 3647 . C . . END=3649 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 3650 . A . . END=3650 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,922 -20_10037292_10066351 3651 . G . . END=3653 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3654 . T . . END=3654 GT:DP:GQ:MIN_DP:PL 0/0:29:60:29:0,60,844 -20_10037292_10066351 3655 . T . . END=3655 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 3656 . C . . END=3658 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 3659 . G . . END=3661 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3662 . C . . END=3662 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,961 -20_10037292_10066351 3663 . A . . END=3666 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,911 -20_10037292_10066351 3667 . G . . END=3667 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,943 -20_10037292_10066351 3668 . A . . END=3668 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 3669 . T . . END=3669 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,897 -20_10037292_10066351 3670 . G . . END=3670 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,889 -20_10037292_10066351 3671 . T . . END=3671 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,947 -20_10037292_10066351 3672 . G . . END=3672 GT:DP:GQ:MIN_DP:PL 0/0:32:77:32:0,77,907 -20_10037292_10066351 3673 . T . . END=3676 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,869 -20_10037292_10066351 3677 . G . . END=3677 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,927 -20_10037292_10066351 3678 . G . . END=3679 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 3680 . A . . END=3680 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,912 -20_10037292_10066351 3681 . G . . END=3684 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,977 -20_10037292_10066351 3685 . T . . END=3687 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3688 . C . . END=3688 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,891 -20_10037292_10066351 3689 . A . . END=3689 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,983 -20_10037292_10066351 3690 . G . . END=3691 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1003 -20_10037292_10066351 3692 . G . . END=3693 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1001 -20_10037292_10066351 3694 . A . . END=3694 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 3695 . G . . END=3695 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1051 -20_10037292_10066351 3696 . A . . END=3700 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 3701 . T . . END=3701 GT:DP:GQ:MIN_DP:PL 0/0:36:79:36:0,79,985 -20_10037292_10066351 3702 . A . . END=3702 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 3703 . T . . END=3703 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1054 -20_10037292_10066351 3704 . G . . END=3704 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 3705 . G . . END=3706 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1107 -20_10037292_10066351 3707 . G . . END=3707 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 3708 . T . . END=3708 GT:DP:GQ:MIN_DP:PL 0/0:37:57:37:0,57,902 -20_10037292_10066351 3709 . G . . END=3715 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 3716 . A . . END=3724 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,1056 -20_10037292_10066351 3725 . G . . END=3725 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1033 -20_10037292_10066351 3726 . A . . END=3726 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 3727 . C . . END=3727 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,925 -20_10037292_10066351 3728 . A . . END=3728 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3729 . C . . END=3729 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,930 -20_10037292_10066351 3730 . G . . END=3732 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,947 -20_10037292_10066351 3733 . A . . END=3733 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1034 -20_10037292_10066351 3734 . A . . END=3736 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1074 -20_10037292_10066351 3737 . A . . END=3742 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 3743 . G . . END=3743 GT:DP:GQ:MIN_DP:PL 0/0:35:83:35:0,83,1077 -20_10037292_10066351 3744 . C . . END=3744 GT:DP:GQ:MIN_DP:PL 0/0:36:59:36:0,59,1005 -20_10037292_10066351 3745 . C . . END=3750 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1058 -20_10037292_10066351 3751 . A . . END=3751 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 3752 . G . . END=3754 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 3755 . T . . END=3755 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1030 -20_10037292_10066351 3756 . G . . END=3758 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 3759 . C . . END=3761 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 3762 . T . . END=3762 GT:DP:GQ:MIN_DP:PL 0/0:37:70:37:0,70,1061 -20_10037292_10066351 3763 . C . . END=3763 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1147 -20_10037292_10066351 3764 . A . . END=3767 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 3768 . G . . END=3768 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1166 -20_10037292_10066351 3769 . A . . END=3770 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 3771 . A . . END=3771 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1049 -20_10037292_10066351 3772 . C . . END=3772 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 3773 . C . . END=3773 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1116 -20_10037292_10066351 3774 . A . . END=3780 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1199 -20_10037292_10066351 3781 . C . . END=3781 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1169 -20_10037292_10066351 3782 . T . . END=3792 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 3793 . T . . END=3795 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3796 . G . . END=3796 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1000 -20_10037292_10066351 3797 . G . . END=3814 GT:DP:GQ:MIN_DP:PL 0/0:35:93:32:0,93,1021 -20_10037292_10066351 3815 . A . . END=3825 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1007 -20_10037292_10066351 3826 . C . . END=3827 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 3828 . T . . END=3848 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 3849 . G . . END=3856 GT:DP:GQ:MIN_DP:PL 0/0:29:78:27:0,78,1170 -20_10037292_10066351 3857 . A . . END=3867 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,816 -20_10037292_10066351 3868 . T . . END=3868 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,891 -20_10037292_10066351 3869 . G . . END=3880 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3881 . C . . END=3882 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,978 -20_10037292_10066351 3883 . G . . END=3883 GT:DP:GQ:MIN_DP:PL 0/0:30:89:30:0,89,918 -20_10037292_10066351 3884 . T . . END=3892 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,994 -20_10037292_10066351 3893 . T . . END=3893 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1072 -20_10037292_10066351 3894 . C . . END=3898 GT:DP:GQ:MIN_DP:PL 0/0:33:93:31:0,93,882 -20_10037292_10066351 3899 . G . . END=3899 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 3900 . C . . END=3903 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 -20_10037292_10066351 3904 . T . . END=3904 GT:DP:GQ:MIN_DP:PL 0/0:36:77:36:0,77,1073 -20_10037292_10066351 3905 . C . . END=3910 GT:DP:GQ:MIN_DP:PL 0/0:37:93:36:0,93,1395 -20_10037292_10066351 3911 . A . . END=3911 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3912 . G . . END=3912 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 3913 . G . . END=3914 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3915 . C . . END=3920 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 3921 . G . . END=3937 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1052 -20_10037292_10066351 3938 . A . . END=3938 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1028 -20_10037292_10066351 3939 . A . . END=3942 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 3943 . T . . END=3949 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 3950 . G . . END=3954 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1050 -20_10037292_10066351 3955 . A . . END=3955 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 3956 . A . . END=3958 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3959 . G . . END=3959 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1117 -20_10037292_10066351 3960 . C . . END=3960 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,902 -20_10037292_10066351 3961 . G . . END=4011 GT:DP:GQ:MIN_DP:PL 0/0:40:99:34:0,102,1024 -20_10037292_10066351 4012 . C T, 1398.06 . DP=44;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=158400,44 GT:AD:DP:GQ:PL:SB 1/1:0,43,0:43:99:1412,129,0,1412,129,1412:0,0,21,22 -20_10037292_10066351 4013 . G . . END=4023 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,106,1268 -20_10037292_10066351 4024 . T . . END=4024 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1212 -20_10037292_10066351 4025 . A . . END=4057 GT:DP:GQ:MIN_DP:PL 0/0:41:99:35:0,102,1223 -20_10037292_10066351 4058 . T . . END=4058 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1090 -20_10037292_10066351 4059 . T . . END=4081 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1106 -20_10037292_10066351 4082 . C . . END=4085 GT:DP:GQ:MIN_DP:PL 0/0:36:96:35:0,96,1440 -20_10037292_10066351 4086 . A . . END=4086 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4087 . T . . END=4089 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 4090 . A . . END=4095 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4096 . T . . END=4114 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 4115 . T . . END=4115 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1024 -20_10037292_10066351 4116 . T . . END=4116 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4117 . A . . END=4119 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 4120 . A . . END=4121 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 4122 . G . . END=4123 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 4124 . G . . END=4131 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,986 -20_10037292_10066351 4132 . T . . END=4133 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,1060 -20_10037292_10066351 4134 . C . . END=4134 GT:DP:GQ:MIN_DP:PL 0/0:32:47:32:0,47,810 -20_10037292_10066351 4135 . G . . END=4136 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 4137 . A . . END=4137 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,899 -20_10037292_10066351 4138 . T . . END=4141 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4142 . A . . END=4142 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1001 -20_10037292_10066351 4143 . T . . END=4149 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 4150 . T . . END=4150 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,947 -20_10037292_10066351 4151 . A . . END=4157 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 4158 . G . . END=4158 GT:DP:GQ:MIN_DP:PL 0/0:32:24:32:0,24,861 -20_10037292_10066351 4159 . G . . END=4159 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,982 -20_10037292_10066351 4160 . A . . END=4164 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1052 -20_10037292_10066351 4165 . A . . END=4167 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 4168 . A . . END=4168 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,1046 -20_10037292_10066351 4169 . C . . END=4169 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 4170 . G . . END=4172 GT:DP:GQ:MIN_DP:PL 0/0:38:96:37:0,96,1440 -20_10037292_10066351 4173 . C . . END=4174 GT:DP:GQ:MIN_DP:PL 0/0:37:75:37:0,75,1090 -20_10037292_10066351 4175 . T . . END=4175 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1052 -20_10037292_10066351 4176 . C . . END=4182 GT:DP:GQ:MIN_DP:PL 0/0:33:91:32:0,91,1105 -20_10037292_10066351 4183 . C . . END=4184 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1094 -20_10037292_10066351 4185 . C . . END=4185 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 4186 . T . . END=4186 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1062 -20_10037292_10066351 4187 . T . . END=4188 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 4189 . T . . END=4189 GT:DP:GQ:MIN_DP:PL 0/0:33:88:33:0,88,1038 -20_10037292_10066351 4190 . G . . END=4202 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 4203 . A . . END=4224 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 4225 . A . . END=4226 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 4227 . T . . END=4234 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4235 . C . . END=4235 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,980 -20_10037292_10066351 4236 . A . . END=4236 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4237 . T . . END=4241 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4242 . G . . END=4242 GT:DP:GQ:MIN_DP:PL 0/0:30:61:30:0,61,914 -20_10037292_10066351 4243 . G . . END=4243 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4244 . T . . END=4244 GT:DP:GQ:MIN_DP:PL 0/0:30:71:30:0,71,911 -20_10037292_10066351 4245 . T . . END=4245 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4246 . G . . END=4249 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,979 -20_10037292_10066351 4250 . G . . END=4255 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 4256 . A . . END=4260 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4261 . G . . END=4263 GT:DP:GQ:MIN_DP:PL 0/0:32:83:31:0,83,1010 -20_10037292_10066351 4264 . T . . END=4264 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4265 . G . . END=4265 GT:DP:GQ:MIN_DP:PL 0/0:33:79:33:0,79,998 -20_10037292_10066351 4266 . T . . END=4269 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 4270 . T . . END=4271 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 4272 . A . . END=4275 GT:DP:GQ:MIN_DP:PL 0/0:34:87:31:0,87,1305 -20_10037292_10066351 4276 . T . . END=4276 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,961 -20_10037292_10066351 4277 . C . . END=4280 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4281 . T . . END=4281 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,942 -20_10037292_10066351 4282 . A . . END=4283 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 4284 . T . . END=4285 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 4286 . T . . END=4286 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 4287 . C . . END=4287 GT:DP:GQ:MIN_DP:PL 0/0:33:59:33:0,59,989 -20_10037292_10066351 4288 . T . . END=4288 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 4289 . A . . END=4293 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 4294 . A . . END=4296 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 4297 . A . . END=4302 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1005 -20_10037292_10066351 4303 . C . . END=4303 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4304 . C . . END=4321 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 4322 . G . . END=4323 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 4324 . A . . END=4329 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 4330 . G . . END=4330 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4331 . A . . END=4331 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,963 -20_10037292_10066351 4332 . C . . END=4332 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1015 -20_10037292_10066351 4333 . C . . END=4333 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4334 . C . . END=4334 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1006 -20_10037292_10066351 4335 . A . . END=4337 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1133 -20_10037292_10066351 4338 . C . . END=4338 GT:DP:GQ:MIN_DP:PL 0/0:36:56:36:0,56,988 -20_10037292_10066351 4339 . C . . END=4339 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1032 -20_10037292_10066351 4340 . T . . END=4340 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4341 . G . . END=4341 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1141 -20_10037292_10066351 4342 . A . . END=4343 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,105,1076 -20_10037292_10066351 4344 . C . . END=4345 GT:DP:GQ:MIN_DP:PL 0/0:37:73:36:0,73,1097 -20_10037292_10066351 4346 . G . . END=4346 GT:DP:GQ:MIN_DP:PL 0/0:36:59:36:0,59,1017 -20_10037292_10066351 4347 . T . . END=4349 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1083 -20_10037292_10066351 4350 . G . . END=4350 GT:DP:GQ:MIN_DP:PL 0/0:37:83:37:0,83,1083 -20_10037292_10066351 4351 . A . . END=4354 GT:DP:GQ:MIN_DP:PL 0/0:37:76:37:0,76,1062 -20_10037292_10066351 4355 . G . . END=4355 GT:DP:GQ:MIN_DP:PL 0/0:37:62:37:0,62,1004 -20_10037292_10066351 4356 . A . . END=4356 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1081 -20_10037292_10066351 4357 . A . . END=4357 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1116 -20_10037292_10066351 4358 . A . . END=4358 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1094 -20_10037292_10066351 4359 . A . . END=4359 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4360 . G . . END=4363 GT:DP:GQ:MIN_DP:PL 0/0:37:73:36:0,73,1042 -20_10037292_10066351 4364 . T . . END=4364 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1082 -20_10037292_10066351 4365 . C . . END=4366 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1056 -20_10037292_10066351 4367 . T . . END=4367 GT:DP:GQ:MIN_DP:PL 0/0:37:63:37:0,63,1057 -20_10037292_10066351 4368 . G . . END=4368 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1014 -20_10037292_10066351 4369 . G . . END=4369 GT:DP:GQ:MIN_DP:PL 0/0:37:65:37:0,65,1058 -20_10037292_10066351 4370 . A . . END=4370 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,1028 -20_10037292_10066351 4371 . G . . END=4375 GT:DP:GQ:MIN_DP:PL 0/0:37:74:36:0,74,1002 -20_10037292_10066351 4376 . T . . END=4376 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,933 -20_10037292_10066351 4377 . T . . END=4377 GT:DP:GQ:MIN_DP:PL 0/0:33:52:33:0,52,895 -20_10037292_10066351 4378 . C . . END=4378 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1050 -20_10037292_10066351 4379 . A . . END=4379 GT:DP:GQ:MIN_DP:PL 0/0:34:53:34:0,53,926 -20_10037292_10066351 4380 . C . . END=4381 GT:DP:GQ:MIN_DP:PL 0/0:34:65:33:0,65,983 -20_10037292_10066351 4382 . T . . END=4382 GT:DP:GQ:MIN_DP:PL 0/0:34:54:34:0,54,901 -20_10037292_10066351 4383 . T . . END=4386 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,976 -20_10037292_10066351 4387 . A . . END=4387 GT:DP:GQ:MIN_DP:PL 0/0:33:40:33:0,40,800 -20_10037292_10066351 4388 . C . . END=4388 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,926 -20_10037292_10066351 4389 . C . . END=4389 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,980 -20_10037292_10066351 4390 . A . . END=4390 GT:DP:GQ:MIN_DP:PL 0/0:34:54:34:0,54,915 -20_10037292_10066351 4391 . T . . END=4391 GT:DP:GQ:MIN_DP:PL 0/0:34:52:34:0,52,819 -20_10037292_10066351 4392 . C . . END=4393 GT:DP:GQ:MIN_DP:PL 0/0:33:62:32:0,62,824 -20_10037292_10066351 4394 . A . . END=4396 GT:DP:GQ:MIN_DP:PL 0/0:36:71:35:0,71,987 -20_10037292_10066351 4397 . T . . END=4398 GT:DP:GQ:MIN_DP:PL 0/0:37:61:36:0,61,1000 -20_10037292_10066351 4399 . A . . END=4399 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 4400 . T . . END=4400 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1063 -20_10037292_10066351 4401 . T . . END=4402 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1098 -20_10037292_10066351 4403 . A . . END=4403 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 4404 . A . . END=4404 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 4405 . A . . END=4405 GT:DP:GQ:MIN_DP:PL 0/0:38:80:38:0,80,1107 -20_10037292_10066351 4406 . C . . END=4406 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,945 -20_10037292_10066351 4407 . A . . END=4407 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4408 . T . . END=4408 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 4409 . A ATG,ATATG, 710.03 . DP=31;ExcessHet=0.0000;MLEAC=0,2,0;MLEAF=0.00,1.00,0.00;RAW_MQandDP=111600,31 GT:AD:DP:GQ:PL:SB 2/2:0,0,21,0:21:69:724,765,1112,69,87,0,767,961,90,918:0,0,10,11 -20_10037292_10066351 4410 . T . . END=4410 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1170 -20_10037292_10066351 4411 . G . . END=4411 GT:DP:GQ:MIN_DP:PL 0/0:39:0:39:0,0,531 -20_10037292_10066351 4412 . T . . END=4419 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1260 -20_10037292_10066351 4420 . T . . END=4426 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 4427 . G . . END=4427 GT:DP:GQ:MIN_DP:PL 0/0:36:74:36:0,74,1020 -20_10037292_10066351 4428 . T . . END=4431 GT:DP:GQ:MIN_DP:PL 0/0:36:84:36:0,84,1260 -20_10037292_10066351 4432 . T . . END=4435 GT:DP:GQ:MIN_DP:PL 0/0:37:90:35:0,90,1350 -20_10037292_10066351 4436 . C . . END=4436 GT:DP:GQ:MIN_DP:PL 0/0:35:0:35:0,0,717 -20_10037292_10066351 4437 . A . . END=4437 GT:DP:GQ:MIN_DP:PL 0/0:35:34:35:0,34,781 -20_10037292_10066351 4438 . T . . END=4438 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 4439 . G . . END=4454 GT:DP:GQ:MIN_DP:PL 0/0:33:81:31:0,81,971 -20_10037292_10066351 4455 . A . . END=4455 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4456 . T . . END=4462 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,927 -20_10037292_10066351 4463 . A . . END=4463 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,936 -20_10037292_10066351 4464 . T . . END=4465 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 4466 . T . . END=4473 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 4474 . A . . END=4474 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,890 -20_10037292_10066351 4475 . G . . END=4475 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,869 -20_10037292_10066351 4476 . A . . END=4476 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,879 -20_10037292_10066351 4477 . C . . END=4484 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,860 -20_10037292_10066351 4485 . C . . END=4485 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,887 -20_10037292_10066351 4486 . A . . END=4487 GT:DP:GQ:MIN_DP:PL 0/0:32:84:31:0,84,1260 -20_10037292_10066351 4488 . G . . END=4488 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,942 -20_10037292_10066351 4489 . G . . END=4491 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 4492 . C . . END=4492 GT:DP:GQ:MIN_DP:PL 0/0:29:56:29:0,56,779 -20_10037292_10066351 4493 . G . . END=4493 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,804 -20_10037292_10066351 4494 . C . . END=4495 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,950 -20_10037292_10066351 4496 . G . . END=4496 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,925 -20_10037292_10066351 4497 . T . . END=4499 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,963 -20_10037292_10066351 4500 . C . . END=4500 GT:DP:GQ:MIN_DP:PL 0/0:29:67:29:0,67,843 -20_10037292_10066351 4501 . A . . END=4504 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 4505 . T . . END=4507 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,952 -20_10037292_10066351 4508 . C . . END=4508 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,892 -20_10037292_10066351 4509 . A . . END=4509 GT:DP:GQ:MIN_DP:PL 0/0:31:73:31:0,73,943 -20_10037292_10066351 4510 . G . . END=4510 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,954 -20_10037292_10066351 4511 . T . . END=4511 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,878 -20_10037292_10066351 4512 . T . . END=4512 GT:DP:GQ:MIN_DP:PL 0/0:31:60:31:0,60,895 -20_10037292_10066351 4513 . C . . END=4513 GT:DP:GQ:MIN_DP:PL 0/0:32:47:32:0,47,858 -20_10037292_10066351 4514 . A . . END=4516 GT:DP:GQ:MIN_DP:PL 0/0:32:62:32:0,62,916 -20_10037292_10066351 4517 . G . . END=4517 GT:DP:GQ:MIN_DP:PL 0/0:32:34:32:0,34,834 -20_10037292_10066351 4518 . C . . END=4518 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,949 -20_10037292_10066351 4519 . A . . END=4519 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,970 -20_10037292_10066351 4520 . A . . END=4520 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,932 -20_10037292_10066351 4521 . C . . END=4521 GT:DP:GQ:MIN_DP:PL 0/0:32:50:32:0,50,885 -20_10037292_10066351 4522 . C . . END=4522 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1000 -20_10037292_10066351 4523 . T . . END=4524 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1056 -20_10037292_10066351 4525 . C . . END=4525 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,931 -20_10037292_10066351 4526 . A . . END=4526 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,862 -20_10037292_10066351 4527 . C . . END=4527 GT:DP:GQ:MIN_DP:PL 0/0:32:49:32:0,49,875 -20_10037292_10066351 4528 . C . . END=4530 GT:DP:GQ:MIN_DP:PL 0/0:33:65:33:0,65,945 -20_10037292_10066351 4531 . C . . END=4533 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 -20_10037292_10066351 4534 . G . . END=4534 GT:DP:GQ:MIN_DP:PL 0/0:33:71:33:0,71,931 -20_10037292_10066351 4535 . G . . END=4548 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,924 -20_10037292_10066351 4549 . C . . END=4555 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,875 -20_10037292_10066351 4556 . C . . END=4564 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 4565 . G . . END=4565 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,769 -20_10037292_10066351 4566 . A . . END=4566 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,945 -20_10037292_10066351 4567 . T . . END=4568 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 4569 . T . . END=4574 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4575 . A . . END=4575 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1044 -20_10037292_10066351 4576 . T . . END=4582 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1077 -20_10037292_10066351 4583 . T . . END=4583 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,949 -20_10037292_10066351 4584 . A . . END=4584 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1036 -20_10037292_10066351 4585 . G . . END=4585 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,992 -20_10037292_10066351 4586 . A . . END=4586 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 4587 . G . . END=4587 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1042 -20_10037292_10066351 4588 . A . . END=4588 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,987 -20_10037292_10066351 4589 . T . . END=4589 GT:DP:GQ:MIN_DP:PL 0/0:35:60:35:0,60,992 -20_10037292_10066351 4590 . G . . END=4590 GT:DP:GQ:MIN_DP:PL 0/0:35:79:35:0,79,1008 -20_10037292_10066351 4591 . G . . END=4591 GT:DP:GQ:MIN_DP:PL 0/0:35:56:35:0,56,909 -20_10037292_10066351 4592 . G . . END=4593 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4594 . T . . END=4594 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,979 -20_10037292_10066351 4595 . T . . END=4596 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4597 . C . . END=4597 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,951 -20_10037292_10066351 4598 . A . . END=4599 GT:DP:GQ:MIN_DP:PL 0/0:35:66:34:0,66,937 -20_10037292_10066351 4600 . C . . END=4600 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,937 -20_10037292_10066351 4601 . A . . END=4603 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1025 -20_10037292_10066351 4604 . T . . END=4604 GT:DP:GQ:MIN_DP:PL 0/0:34:80:34:0,80,1029 -20_10037292_10066351 4605 . T . . END=4605 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 4606 . G . . END=4606 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,938 -20_10037292_10066351 4607 . G . . END=4607 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,966 -20_10037292_10066351 4608 . C . . END=4611 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 4612 . G . . END=4612 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,998 -20_10037292_10066351 4613 . C . . END=4616 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 4617 . T . . END=4620 GT:DP:GQ:MIN_DP:PL 0/0:33:81:28:0,81,853 -20_10037292_10066351 4621 . G . . END=4621 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4622 . A . . END=4626 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 4627 . C . . END=4627 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4628 . T . . END=4630 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 4631 . C . . END=4631 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4632 . C . . END=4632 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,940 -20_10037292_10066351 4633 . T . . END=4633 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4634 . C . . END=4634 GT:DP:GQ:MIN_DP:PL 0/0:31:60:31:0,60,922 -20_10037292_10066351 4635 . A . . END=4635 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,947 -20_10037292_10066351 4636 . A . . END=4636 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,1000 -20_10037292_10066351 4637 . G . . END=4637 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4638 . T . . END=4638 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,947 -20_10037292_10066351 4639 . G . . END=4639 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,968 -20_10037292_10066351 4640 . A . . END=4642 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4643 . C . . END=4644 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 4645 . C . . END=4649 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 4650 . T . . END=4650 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,874 -20_10037292_10066351 4651 . T . . END=4654 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,1080 -20_10037292_10066351 4655 . C . . END=4655 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,1035 -20_10037292_10066351 4656 . C . . END=4666 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,759 -20_10037292_10066351 4667 . C . . END=4668 GT:DP:GQ:MIN_DP:PL 0/0:27:61:26:0,61,735 -20_10037292_10066351 4669 . G . . END=4671 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,870 -20_10037292_10066351 4672 . A . . END=4672 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,840 -20_10037292_10066351 4673 . T . . END=4674 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,854 -20_10037292_10066351 4675 . A . . END=4675 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 4676 . C . . END=4677 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,802 -20_10037292_10066351 4678 . G . . END=4678 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,893 -20_10037292_10066351 4679 . G . . END=4686 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 4687 . C . . END=4687 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,884 -20_10037292_10066351 4688 . A . . END=4694 GT:DP:GQ:MIN_DP:PL 0/0:30:81:27:0,81,769 -20_10037292_10066351 4695 . C . . END=4695 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,879 -20_10037292_10066351 4696 . T . . END=4697 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 4698 . G . . END=4703 GT:DP:GQ:MIN_DP:PL 0/0:32:75:31:0,75,892 -20_10037292_10066351 4704 . A . . END=4709 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 4710 . T . . END=4711 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,855 -20_10037292_10066351 4712 . G . . END=4715 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 4716 . T . . END=4716 GT:DP:GQ:MIN_DP:PL 0/0:33:55:33:0,55,937 -20_10037292_10066351 4717 . T . . END=4724 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1084 -20_10037292_10066351 4725 . C . . END=4725 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1064 -20_10037292_10066351 4726 . A . . END=4735 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,111,1264 -20_10037292_10066351 4736 . A . . END=4736 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1108 -20_10037292_10066351 4737 . C . . END=4749 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,111,1303 -20_10037292_10066351 4750 . C . . END=4750 GT:DP:GQ:MIN_DP:PL 0/0:42:96:42:0,96,1256 -20_10037292_10066351 4751 . T . . END=4790 GT:DP:GQ:MIN_DP:PL 0/0:44:99:41:0,104,1266 -20_10037292_10066351 4791 . G . . END=4791 GT:DP:GQ:MIN_DP:PL 0/0:45:78:45:0,78,1259 -20_10037292_10066351 4792 . A . . END=4802 GT:DP:GQ:MIN_DP:PL 0/0:45:99:44:0,107,1378 -20_10037292_10066351 4803 . A . . END=4803 GT:DP:GQ:MIN_DP:PL 0/0:44:83:44:0,83,1198 -20_10037292_10066351 4804 . A . . END=4810 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,114,1431 -20_10037292_10066351 4811 . T . . END=4811 GT:DP:GQ:MIN_DP:PL 0/0:45:79:45:0,79,1233 -20_10037292_10066351 4812 . A . . END=4831 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,101,1192 -20_10037292_10066351 4832 . C . . END=4833 GT:DP:GQ:MIN_DP:PL 0/0:43:95:43:0,95,1171 -20_10037292_10066351 4834 . C . . END=4849 GT:DP:GQ:MIN_DP:PL 0/0:43:99:39:0,99,1131 -20_10037292_10066351 4850 . A . . END=4851 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1137 -20_10037292_10066351 4852 . T . . END=4854 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 4855 . C . . END=4855 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1139 -20_10037292_10066351 4856 . T . . END=4859 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,1170 -20_10037292_10066351 4860 . T . . END=4866 GT:DP:GQ:MIN_DP:PL 0/0:36:81:34:0,81,1215 -20_10037292_10066351 4867 . T . . END=4876 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,1080 -20_10037292_10066351 4877 . G . . END=4887 GT:DP:GQ:MIN_DP:PL 0/0:26:63:25:0,63,766 -20_10037292_10066351 4888 . A . . END=4890 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 4891 . T . . END=4893 GT:DP:GQ:MIN_DP:PL 0/0:25:66:25:0,66,990 -20_10037292_10066351 4894 . C . . END=4894 GT:DP:GQ:MIN_DP:PL 0/0:25:59:25:0,59,757 -20_10037292_10066351 4895 . T . . END=4899 GT:DP:GQ:MIN_DP:PL 0/0:25:60:24:0,60,900 -20_10037292_10066351 4900 . A . . END=4913 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,813 -20_10037292_10066351 4914 . G . . END=4914 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 -20_10037292_10066351 4915 . G . . END=4915 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 4916 . G . . END=4919 GT:DP:GQ:MIN_DP:PL 0/0:27:65:26:0,65,769 -20_10037292_10066351 4920 . T . . END=4924 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 4925 . T . . END=4925 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 4926 . G . . END=4926 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 4927 . C . . END=4927 GT:DP:GQ:MIN_DP:PL 0/0:25:28:25:0,28,665 -20_10037292_10066351 4928 . A . . END=4928 GT:DP:GQ:MIN_DP:PL 0/0:25:47:25:0,47,725 -20_10037292_10066351 4929 . A . . END=4935 GT:DP:GQ:MIN_DP:PL 0/0:25:69:24:0,69,1035 -20_10037292_10066351 4936 . T . . END=4936 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,709 -20_10037292_10066351 4937 . A . . END=4939 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 4940 . A . . END=4940 GT:DP:GQ:MIN_DP:PL 0/0:24:56:24:0,56,727 -20_10037292_10066351 4941 . A . . END=4941 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4942 . G . . END=4942 GT:DP:GQ:MIN_DP:PL 0/0:24:40:24:0,40,714 -20_10037292_10066351 4943 . A . . END=4943 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4944 . A . . END=4949 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,737 -20_10037292_10066351 4950 . A . . END=4950 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 4951 . T . . END=4951 GT:DP:GQ:MIN_DP:PL 0/0:24:56:24:0,56,685 -20_10037292_10066351 4952 . G . . END=4952 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 4953 . T . . END=4953 GT:DP:GQ:MIN_DP:PL 0/0:25:62:25:0,62,712 -20_10037292_10066351 4954 . C . . END=4959 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 4960 . A . . END=4962 GT:DP:GQ:MIN_DP:PL 0/0:29:84:28:0,84,876 -20_10037292_10066351 4963 . A . . END=4963 GT:DP:GQ:MIN_DP:PL 0/0:30:62:30:0,62,862 -20_10037292_10066351 4964 . G . . END=4966 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,955 -20_10037292_10066351 4967 . A . . END=4968 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 4969 . G . . END=4969 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,959 -20_10037292_10066351 4970 . C . . END=4970 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 4971 . A . . END=4971 GT:DP:GQ:MIN_DP:PL 0/0:30:44:30:0,44,863 -20_10037292_10066351 4972 . G . . END=4972 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,921 -20_10037292_10066351 4973 . A . . END=4976 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 4977 . A . . END=4977 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,903 -20_10037292_10066351 4978 . A . . END=4989 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,860 -20_10037292_10066351 4990 . T . . END=4990 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,837 -20_10037292_10066351 4991 . C . . END=5000 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 5001 . G . . END=5011 GT:DP:GQ:MIN_DP:PL 0/0:28:71:27:0,71,806 -20_10037292_10066351 5012 . A . . END=5012 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,831 -20_10037292_10066351 5013 . G . . END=5018 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 5019 . C . . END=5019 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,798 -20_10037292_10066351 5020 . A . . END=5026 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,793 -20_10037292_10066351 5027 . C T, 784.06 . DP=27;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=97200,27 GT:AD:DP:GQ:PL:SB 1/1:0,26,0:26:77:798,77,0,798,77,798:0,0,13,13 -20_10037292_10066351 5028 . C . . END=5037 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,905 -20_10037292_10066351 5038 . T . . END=5044 GT:DP:GQ:MIN_DP:PL 0/0:26:62:25:0,62,765 -20_10037292_10066351 5045 . G . . END=5045 GT:DP:GQ:MIN_DP:PL 0/0:27:58:27:0,58,808 -20_10037292_10066351 5046 . A . . END=5049 GT:DP:GQ:MIN_DP:PL 0/0:26:63:23:0,63,681 -20_10037292_10066351 5050 . T . . END=5050 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,633 -20_10037292_10066351 5051 . T . . END=5051 GT:DP:GQ:MIN_DP:PL 0/0:24:59:24:0,59,681 -20_10037292_10066351 5052 . G . . END=5055 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,722 -20_10037292_10066351 5056 . G . . END=5056 GT:DP:GQ:MIN_DP:PL 0/0:25:62:25:0,62,771 -20_10037292_10066351 5057 . A . . END=5057 GT:DP:GQ:MIN_DP:PL 0/0:25:75:25:0,75,713 -20_10037292_10066351 5058 . T . . END=5058 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,732 -20_10037292_10066351 5059 . G . . END=5059 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 5060 . A . . END=5060 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,709 -20_10037292_10066351 5061 . A . . END=5061 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,776 -20_10037292_10066351 5062 . T . . END=5063 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,874 -20_10037292_10066351 5064 . G . . END=5064 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,871 -20_10037292_10066351 5065 . A . . END=5069 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,838 -20_10037292_10066351 5070 . C . . END=5071 GT:DP:GQ:MIN_DP:PL 0/0:28:62:28:0,62,836 -20_10037292_10066351 5072 . G . . END=5072 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 5073 . A . . END=5074 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,851 -20_10037292_10066351 5075 . G . . END=5075 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,811 -20_10037292_10066351 5076 . T . . END=5078 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 5079 . G . . END=5079 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,837 -20_10037292_10066351 5080 . T . . END=5080 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 5081 . C . . END=5081 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,867 -20_10037292_10066351 5082 . C . . END=5087 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 5088 . A . . END=5088 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 5089 . G . . END=5095 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 5096 . G . . END=5097 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 5098 . A . . END=5103 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 5104 . C . . END=5106 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 5107 . G . . END=5108 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 5109 . T . . END=5109 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,899 -20_10037292_10066351 5110 . A . . END=5110 GT:DP:GQ:MIN_DP:PL 0/0:29:59:29:0,59,846 -20_10037292_10066351 5111 . C . . END=5129 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,876 -20_10037292_10066351 5130 . A . . END=5130 GT:DP:GQ:MIN_DP:PL 0/0:28:65:28:0,65,831 -20_10037292_10066351 5131 . T . . END=5134 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,843 -20_10037292_10066351 5135 . C . . END=5141 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,949 -20_10037292_10066351 5142 . C . . END=5142 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,965 -20_10037292_10066351 5143 . T . . END=5149 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 5150 . G . . END=5171 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,906 -20_10037292_10066351 5172 . C . . END=5172 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,921 -20_10037292_10066351 5173 . C . . END=5176 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 5177 . C . . END=5183 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 5184 . G . . END=5184 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,946 -20_10037292_10066351 5185 . C . . END=5189 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 5190 . T . . END=5190 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5191 . G . . END=5193 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5194 . T . . END=5196 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5197 . G . . END=5210 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 5211 . A . . END=5468 GT:DP:GQ:MIN_DP:PL 0/0:46:99:36:0,99,1192 -20_10037292_10066351 5469 . A G, 1297.06 . DP=42;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=151200,42 GT:AD:DP:GQ:PL:SB 1/1:0,42,0:42:99:1311,126,0,1311,126,1311:0,0,18,24 -20_10037292_10066351 5470 . G . . END=5495 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,111,1345 -20_10037292_10066351 7536 . C . . END=7552 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,107,1241 -20_10037292_10066351 7553 . A . . END=7553 GT:DP:GQ:MIN_DP:PL 0/0:41:78:41:0,78,1102 -20_10037292_10066351 7554 . A . . END=7555 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,102,1209 -20_10037292_10066351 7556 . C . . END=7556 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1063 -20_10037292_10066351 7557 . A G, 935.06 . DP=36;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=129600,36 GT:AD:DP:GQ:PL:SB 1/1:0,34,0:34:99:949,100,0,949,100,949:0,0,17,17 -20_10037292_10066351 7558 . C . . END=7558 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 7559 . T . . END=7559 GT:DP:GQ:MIN_DP:PL 0/0:38:94:38:0,94,1183 -20_10037292_10066351 7560 . C . . END=7569 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7570 . C . . END=7570 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1111 -20_10037292_10066351 7571 . A . . END=7573 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1138 -20_10037292_10066351 7574 . T . . END=7574 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1087 -20_10037292_10066351 7575 . T . . END=7579 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1069 -20_10037292_10066351 7580 . C . . END=7580 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1164 -20_10037292_10066351 7581 . T . . END=7581 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 7582 . T . . END=7582 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1088 -20_10037292_10066351 7583 . C . . END=7584 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 7585 . G . . END=7585 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 7586 . A . . END=7595 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,99,1485 -20_10037292_10066351 7596 . A . . END=7601 GT:DP:GQ:MIN_DP:PL 0/0:37:96:36:0,96,1440 -20_10037292_10066351 7602 . G . . END=7610 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7611 . A . . END=7611 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1069 -20_10037292_10066351 7612 . G . . END=7614 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1207 -20_10037292_10066351 7615 . C . . END=7615 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1080 -20_10037292_10066351 7616 . A . . END=7618 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 7619 . T . . END=7630 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1395 -20_10037292_10066351 7631 . T . . END=7632 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 7633 . A . . END=7633 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1005 -20_10037292_10066351 7634 . G . . END=7649 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 7650 . A . . END=7650 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1034 -20_10037292_10066351 7651 . C . . END=7657 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 7658 . T . . END=7658 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,981 -20_10037292_10066351 7659 . G . . END=7665 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 7666 . A . . END=7667 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 7668 . C . . END=7668 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 7669 . C . . END=7679 GT:DP:GQ:MIN_DP:PL 0/0:31:82:29:0,82,996 -20_10037292_10066351 7680 . A . . END=7680 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,895 -20_10037292_10066351 7681 . C . . END=7684 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 7685 . G . . END=7685 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,993 -20_10037292_10066351 7686 . T . . END=7686 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 7687 . T . . END=7687 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1008 -20_10037292_10066351 7688 . A . . END=7690 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 7691 . C . . END=7691 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,974 -20_10037292_10066351 7692 . C . . END=7695 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,936 -20_10037292_10066351 7696 . T . . END=7696 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,929 -20_10037292_10066351 7697 . A . . END=7705 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,990 -20_10037292_10066351 7706 . C . . END=7706 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,895 -20_10037292_10066351 7707 . A . . END=7708 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 7709 . T . . END=7709 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,937 -20_10037292_10066351 7710 . C . . END=7712 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 7713 . T . . END=7713 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1093 -20_10037292_10066351 7714 . A . . END=7714 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7715 . C . . END=7715 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1058 -20_10037292_10066351 7716 . A . . END=7718 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7719 . C . . END=7719 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1091 -20_10037292_10066351 7720 . C . . END=7723 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 7724 . A . . END=7724 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1138 -20_10037292_10066351 7725 . C . . END=7730 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 7731 . A . . END=7742 GT:DP:GQ:MIN_DP:PL 0/0:36:90:32:0,90,1350 -20_10037292_10066351 7743 . A . . END=7744 GT:DP:GQ:MIN_DP:PL 0/0:33:84:32:0,84,1260 -20_10037292_10066351 7745 . A . . END=7748 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1131 -20_10037292_10066351 7749 . T . . END=7751 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 7752 . C . . END=7752 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1118 -20_10037292_10066351 7753 . T . . END=7753 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 7754 . C . . END=7754 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1032 -20_10037292_10066351 7755 . C . . END=7763 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 7764 . T . . END=7764 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1019 -20_10037292_10066351 7765 . T . . END=7769 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 7770 . C . . END=7774 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 7775 . A . . END=7775 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1053 -20_10037292_10066351 7776 . A . . END=7780 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 7781 . A . . END=7785 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1115 -20_10037292_10066351 7786 . G T, 1043.06 . DP=35;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=126000,35 GT:AD:DP:GQ:PL:SB 1/1:0,34,0:34:99:1057,102,0,1057,102,1057:0,0,19,15 -20_10037292_10066351 7787 . C . . END=7795 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 7796 . A . . END=7796 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1024 -20_10037292_10066351 7797 . A . . END=7798 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 7799 . T . . END=7799 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1065 -20_10037292_10066351 7800 . C . . END=7812 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,102,1061 -20_10037292_10066351 7813 . T . . END=7813 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,1099 -20_10037292_10066351 7814 . T . . END=7859 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1254 -20_10037292_10066351 7860 . G . . END=7860 GT:DP:GQ:MIN_DP:PL 0/0:42:95:42:0,95,1293 -20_10037292_10066351 7861 . A . . END=7863 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,108,1620 -20_10037292_10066351 7864 . G . . END=7864 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1148 -20_10037292_10066351 7865 . C . . END=7873 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 7874 . G . . END=7874 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1195 -20_10037292_10066351 7875 . A . . END=7879 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 7880 . T . . END=7887 GT:DP:GQ:MIN_DP:PL 0/0:35:93:33:0,93,1395 -20_10037292_10066351 7888 . A . . END=7888 GT:DP:GQ:MIN_DP:PL 0/0:34:74:34:0,74,1071 -20_10037292_10066351 7889 . A . . END=7894 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 7895 . C . . END=7895 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1094 -20_10037292_10066351 7896 . C . . END=7909 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1011 -20_10037292_10066351 7910 . G . . END=7918 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,1215 -20_10037292_10066351 7919 . G . . END=7919 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,968 -20_10037292_10066351 7920 . T . . END=7926 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 7927 . A . . END=7929 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1003 -20_10037292_10066351 7930 . G . . END=7930 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,970 -20_10037292_10066351 7931 . A . . END=7933 GT:DP:GQ:MIN_DP:PL 0/0:34:90:30:0,90,986 -20_10037292_10066351 7934 . A . . END=7951 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1485 -20_10037292_10066351 7952 . T . . END=7952 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1244 -20_10037292_10066351 7953 . G . . END=7963 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,100,1172 -20_10037292_10066351 7964 . T . . END=7964 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 7965 . T . . END=7967 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 7968 . C . . END=7968 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1440 -20_10037292_10066351 7969 . T . . END=7975 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 7976 . T . . END=7976 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1161 -20_10037292_10066351 7977 . A . . END=7986 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,101,1160 -20_10037292_10066351 7987 . T . . END=7987 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1081 -20_10037292_10066351 7988 . G . . END=7990 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 7991 . G . . END=7991 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1134 -20_10037292_10066351 7992 . A . . END=8011 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1155 -20_10037292_10066351 8012 . A . . END=8012 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1234 -20_10037292_10066351 8013 . A . . END=8079 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,99,1221 -20_10037292_10066351 8080 . C . . END=8083 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 8084 . G . . END=8086 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 8087 . A . . END=8093 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8094 . A . . END=8096 GT:DP:GQ:MIN_DP:PL 0/0:34:81:34:0,81,992 -20_10037292_10066351 8097 . A . . END=8098 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 8099 . T . . END=8099 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,989 -20_10037292_10066351 8100 . A . . END=8102 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1064 -20_10037292_10066351 8103 . A . . END=8103 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1037 -20_10037292_10066351 8104 . A . . END=8104 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1037 -20_10037292_10066351 8105 . A . . END=8105 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1022 -20_10037292_10066351 8106 . T . . END=8106 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8107 . G . . END=8109 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1018 -20_10037292_10066351 8110 . C . . END=8117 GT:DP:GQ:MIN_DP:PL 0/0:33:75:28:0,75,1125 -20_10037292_10066351 8118 . A . . END=8121 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 8122 . G . . END=8130 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,945 -20_10037292_10066351 8131 . A . . END=8131 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8132 . C . . END=8132 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,970 -20_10037292_10066351 8133 . A . . END=8135 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,954 -20_10037292_10066351 8136 . C . . END=8140 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 8141 . G . . END=8141 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8142 . A . . END=8144 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8145 . T . . END=8150 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8151 . A . . END=8156 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8157 . C . . END=8157 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 8158 . C . . END=8180 GT:DP:GQ:MIN_DP:PL 0/0:28:70:26:0,70,854 -20_10037292_10066351 8181 . A . . END=8181 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,812 -20_10037292_10066351 8182 . T . . END=8204 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,730 -20_10037292_10066351 8205 . G . . END=8205 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,702 -20_10037292_10066351 8206 . T . . END=8206 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,1125 -20_10037292_10066351 8207 . C . . END=8207 GT:DP:GQ:MIN_DP:PL 0/0:26:62:26:0,62,793 -20_10037292_10066351 8208 . C . . END=8209 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 8210 . T . . END=8210 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,868 -20_10037292_10066351 8211 . T . . END=8216 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 8217 . A . . END=8223 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,854 -20_10037292_10066351 8224 . T . . END=8229 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8230 . A . . END=8235 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1055 -20_10037292_10066351 8236 . G . . END=8236 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,999 -20_10037292_10066351 8237 . C . . END=8240 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8241 . A . . END=8241 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1044 -20_10037292_10066351 8242 . C . . END=8247 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 8248 . T . . END=8250 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1103 -20_10037292_10066351 8251 . C . . END=8251 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1026 -20_10037292_10066351 8252 . C . . END=8258 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,102,1121 -20_10037292_10066351 8259 . T . . END=8259 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1226 -20_10037292_10066351 8260 . T . . END=8261 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 8262 . T . . END=8269 GT:DP:GQ:MIN_DP:PL 0/0:38:93:36:0,93,1395 -20_10037292_10066351 8270 . C . . END=8270 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,1122 -20_10037292_10066351 8271 . T . . END=8272 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 8273 . T . . END=8274 GT:DP:GQ:MIN_DP:PL 0/0:34:80:34:0,80,1002 -20_10037292_10066351 8275 . T . . END=8276 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,1073 -20_10037292_10066351 8277 . G . . END=8277 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,1011 -20_10037292_10066351 8278 . C . . END=8278 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1007 -20_10037292_10066351 8279 . C . . END=8279 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,970 -20_10037292_10066351 8280 . A . . END=8280 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1088 -20_10037292_10066351 8281 . T . . END=8282 GT:DP:GQ:MIN_DP:PL 0/0:34:82:33:0,82,1000 -20_10037292_10066351 8283 . C . . END=8285 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1075 -20_10037292_10066351 8286 . T . . END=8286 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1030 -20_10037292_10066351 8287 . T . . END=8292 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8293 . C . . END=8293 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1030 -20_10037292_10066351 8294 . A . . END=8296 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8297 . A . . END=8297 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 8298 . C . . END=8298 GT:DP:GQ:MIN_DP:PL 0/0:36:74:36:0,74,1031 -20_10037292_10066351 8299 . T . . END=8299 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1109 -20_10037292_10066351 8300 . C . . END=8305 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1167 -20_10037292_10066351 8306 . A . . END=8307 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1113 -20_10037292_10066351 8308 . C . . END=8308 GT:DP:GQ:MIN_DP:PL 0/0:34:72:34:0,72,991 -20_10037292_10066351 8309 . A . . END=8310 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8311 . C . . END=8311 GT:DP:GQ:MIN_DP:PL 0/0:34:70:34:0,70,951 -20_10037292_10066351 8312 . A . . END=8314 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8315 . C . . END=8332 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,990 -20_10037292_10066351 8333 . T . . END=8333 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1016 -20_10037292_10066351 8334 . A . . END=8335 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8336 . G . . END=8336 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1037 -20_10037292_10066351 8337 . A . . END=8337 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 8338 . C . . END=8338 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1023 -20_10037292_10066351 8339 . T . . END=8339 GT:DP:GQ:MIN_DP:PL 0/0:36:69:36:0,69,1050 -20_10037292_10066351 8340 . T . . END=8340 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1102 -20_10037292_10066351 8341 . A . . END=8341 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8342 . G . . END=8342 GT:DP:GQ:MIN_DP:PL 0/0:36:88:36:0,88,1074 -20_10037292_10066351 8343 . A . . END=8349 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,117,1755 -20_10037292_10066351 8350 . G C, 1162.06 . DP=39;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=140400,39 GT:AD:DP:GQ:PL:SB 1/1:0,39,0:39:99:1176,115,0,1176,115,1176:0,0,16,23 -20_10037292_10066351 8351 . A . . END=8355 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,114,1710 -20_10037292_10066351 8356 . T . . END=8356 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1267 -20_10037292_10066351 8357 . T . . END=8357 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1620 -20_10037292_10066351 8358 . A . . END=8358 GT:DP:GQ:MIN_DP:PL 0/0:41:94:41:0,94,1232 -20_10037292_10066351 8359 . A . . END=8365 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,99,1210 -20_10037292_10066351 8366 . A . . END=8367 GT:DP:GQ:MIN_DP:PL 0/0:38:96:37:0,96,1440 -20_10037292_10066351 8368 . T . . END=8368 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 8369 . T . . END=8369 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1156 -20_10037292_10066351 8370 . C . . END=8378 GT:DP:GQ:MIN_DP:PL 0/0:39:99:34:0,99,1485 -20_10037292_10066351 8379 . G . . END=8388 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8389 . G . . END=8394 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 8395 . A . . END=8396 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8397 . G . . END=8400 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 8401 . A . . END=8401 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,920 -20_10037292_10066351 8402 . A . . END=8408 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,947 -20_10037292_10066351 8409 . C . . END=8425 GT:DP:GQ:MIN_DP:PL 0/0:29:72:27:0,72,1080 -20_10037292_10066351 8426 . C . . END=8426 GT:DP:GQ:MIN_DP:PL 0/0:27:36:27:0,36,772 -20_10037292_10066351 8427 . T . . END=8428 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 8429 . T . . END=8438 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 8439 . G . . END=8439 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,935 -20_10037292_10066351 8440 . C . . END=8440 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 8441 . T . . END=8458 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,938 -20_10037292_10066351 8459 . G . . END=8483 GT:DP:GQ:MIN_DP:PL 0/0:40:99:35:0,102,1192 -20_10037292_10066351 8484 . T . . END=8501 GT:DP:GQ:MIN_DP:PL 0/0:38:90:30:0,90,944 -20_10037292_10066351 8502 . A . . END=8512 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8513 . G . . END=8513 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,919 -20_10037292_10066351 8514 . A . . END=8521 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,956 -20_10037292_10066351 8522 . A . . END=8529 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,934 -20_10037292_10066351 8530 . C . . END=8530 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,911 -20_10037292_10066351 8531 . C . . END=8537 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,980 -20_10037292_10066351 8538 . A . . END=8549 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 8550 . A . . END=8556 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 8557 . A . . END=8576 GT:DP:GQ:MIN_DP:PL 0/0:36:99:33:0,99,1007 -20_10037292_10066351 8577 . G . . END=8581 GT:DP:GQ:MIN_DP:PL 0/0:37:93:35:0,93,1087 -20_10037292_10066351 8582 . C . . END=8584 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8585 . T . . END=8587 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 8588 . C . . END=8591 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 8592 . T . . END=8592 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1049 -20_10037292_10066351 8593 . G . . END=8595 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1040 -20_10037292_10066351 8596 . C . . END=8599 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 8600 . T . . END=8606 GT:DP:GQ:MIN_DP:PL 0/0:34:84:33:0,84,1260 -20_10037292_10066351 8607 . C . . END=8609 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,1170 -20_10037292_10066351 8610 . G . . END=8611 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8612 . T . . END=8613 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 8614 . G . . END=8620 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8621 . C . . END=8621 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,915 -20_10037292_10066351 8622 . A . . END=8623 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,864 -20_10037292_10066351 8624 . T . . END=8624 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,872 -20_10037292_10066351 8625 . G . . END=8633 GT:DP:GQ:MIN_DP:PL 0/0:30:84:28:0,84,928 -20_10037292_10066351 8634 . T . . END=8634 GT:DP:GQ:MIN_DP:PL 0/0:28:63:28:0,63,877 -20_10037292_10066351 8635 . G . . END=8637 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8638 . T . . END=8638 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,847 -20_10037292_10066351 8639 . C . . END=8644 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8645 . T . . END=8645 GT:DP:GQ:MIN_DP:PL 0/0:28:53:28:0,53,770 -20_10037292_10066351 8646 . C . . END=8646 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,950 -20_10037292_10066351 8647 . T . . END=8668 GT:DP:GQ:MIN_DP:PL 0/0:33:90:30:0,90,922 -20_10037292_10066351 8669 . C . . END=8672 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8673 . A . . END=8673 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8674 . G . . END=8674 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1037 -20_10037292_10066351 8675 . G . . END=8676 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8677 . C . . END=8678 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 8679 . C . . END=8683 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 8684 . T . . END=8684 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1090 -20_10037292_10066351 8685 . T . . END=8702 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1065 -20_10037292_10066351 8703 . T . . END=8703 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8704 . T . . END=8704 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1041 -20_10037292_10066351 8705 . T . . END=8720 GT:DP:GQ:MIN_DP:PL 0/0:35:90:33:0,90,1064 -20_10037292_10066351 8721 . A . . END=8725 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8726 . A . . END=8728 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8729 . A . . END=8736 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,928 -20_10037292_10066351 8737 . T . . END=8741 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8742 . A . . END=8742 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,952 -20_10037292_10066351 8743 . A . . END=8745 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,980 -20_10037292_10066351 8746 . C . . END=8746 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,822 -20_10037292_10066351 8747 . A . . END=8747 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,986 -20_10037292_10066351 8748 . C . . END=8749 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 8750 . A . . END=8751 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,979 -20_10037292_10066351 8752 . A . . END=8753 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 8754 . T . . END=8754 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,929 -20_10037292_10066351 8755 . G . . END=8757 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 8758 . A . . END=8758 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1005 -20_10037292_10066351 8759 . C . . END=8770 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 8771 . T . . END=8771 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,819 -20_10037292_10066351 8772 . G . . END=8773 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8774 . G . . END=8774 GT:DP:GQ:MIN_DP:PL 0/0:33:71:33:0,71,962 -20_10037292_10066351 8775 . C . . END=8775 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8776 . T . . END=8776 GT:DP:GQ:MIN_DP:PL 0/0:33:52:33:0,52,865 -20_10037292_10066351 8777 . C . . END=8778 GT:DP:GQ:MIN_DP:PL 0/0:34:82:33:0,82,789 -20_10037292_10066351 8779 . C . . END=8779 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,883 -20_10037292_10066351 8780 . A . . END=8781 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,114,1174 -20_10037292_10066351 8782 . G . . END=8782 GT:DP:GQ:MIN_DP:PL 0/0:37:33:37:0,33,916 -20_10037292_10066351 8783 . A . . END=8791 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1182 -20_10037292_10066351 8792 . G . . END=8792 GT:DP:GQ:MIN_DP:PL 0/0:39:78:39:0,78,1074 -20_10037292_10066351 8793 . G . . END=8800 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1039 -20_10037292_10066351 8801 . T . . END=8801 GT:DP:GQ:MIN_DP:PL 0/0:40:81:40:0,81,1090 -20_10037292_10066351 8802 . T . . END=8802 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,106,1067 -20_10037292_10066351 8803 . C . . END=8803 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,984 -20_10037292_10066351 8804 . C . . END=8804 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,102,1041 -20_10037292_10066351 8805 . C . . END=8805 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,986 -20_10037292_10066351 8806 . C . . END=8806 GT:DP:GQ:MIN_DP:PL 0/0:38:79:38:0,79,1019 -20_10037292_10066351 8807 . A . . END=8813 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,111,1665 -20_10037292_10066351 8814 . G . . END=8814 GT:DP:GQ:MIN_DP:PL 0/0:40:76:40:0,76,1133 -20_10037292_10066351 8815 . A . . END=8816 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 8817 . T . . END=8817 GT:DP:GQ:MIN_DP:PL 0/0:39:39:39:0,39,868 -20_10037292_10066351 8818 . T . . END=8826 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1002 -20_10037292_10066351 8827 . T . . END=8827 GT:DP:GQ:MIN_DP:PL 0/0:38:75:38:0,75,1016 -20_10037292_10066351 8828 . G . . END=8828 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 8829 . G . . END=8831 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 8832 . A . . END=8834 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 8835 . C . . END=8835 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,892 -20_10037292_10066351 8836 . A . . END=8836 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8837 . G . . END=8837 GT:DP:GQ:MIN_DP:PL 0/0:35:61:35:0,61,962 -20_10037292_10066351 8838 . A . . END=8841 GT:DP:GQ:MIN_DP:PL 0/0:35:96:33:0,96,1440 -20_10037292_10066351 8842 . A . . END=8843 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 8844 . A . . END=8844 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1120 -20_10037292_10066351 8845 . A . . END=8845 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8846 . G . . END=8846 GT:DP:GQ:MIN_DP:PL 0/0:36:74:36:0,74,1003 -20_10037292_10066351 8847 . G . . END=8847 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1017 -20_10037292_10066351 8848 . G . . END=8848 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1030 -20_10037292_10066351 8849 . A . . END=8849 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1039 -20_10037292_10066351 8850 . A . . END=8856 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 8857 . A . . END=8857 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1039 -20_10037292_10066351 8858 . G . . END=8858 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,999 -20_10037292_10066351 8859 . G . . END=8860 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 8861 . A . . END=8861 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1118 -20_10037292_10066351 8862 . G . . END=8862 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 8863 . G . . END=8863 GT:DP:GQ:MIN_DP:PL 0/0:37:91:37:0,91,1058 -20_10037292_10066351 8864 . G . . END=8864 GT:DP:GQ:MIN_DP:PL 0/0:37:85:37:0,85,1033 -20_10037292_10066351 8865 . G . . END=8869 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1530 -20_10037292_10066351 8870 . G . . END=8870 GT:DP:GQ:MIN_DP:PL 0/0:38:78:38:0,78,1017 -20_10037292_10066351 8871 . G . . END=8871 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1039 -20_10037292_10066351 8872 . A . . END=8880 GT:DP:GQ:MIN_DP:PL 0/0:37:93:36:0,93,1054 -20_10037292_10066351 8881 . A . . END=8881 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1054 -20_10037292_10066351 8882 . A . . END=8882 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 8883 . A . . END=8883 GT:DP:GQ:MIN_DP:PL 0/0:37:87:37:0,87,1305 -20_10037292_10066351 8884 . G . . END=8884 GT:DP:GQ:MIN_DP:PL 0/0:36:77:36:0,77,1086 -20_10037292_10066351 8885 . A . . END=8885 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,966 -20_10037292_10066351 8886 . AAGAAAGAAAG A, 1268.03 . DP=34;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=122400,34 GT:AD:DP:GQ:PL:SB 1/1:0,29,0:29:88:1282,88,0,1282,88,1282:0,0,17,12 -20_10037292_10066351 8897 . A . . END=8903 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 -20_10037292_10066351 8904 . A . . END=8904 GT:DP:GQ:MIN_DP:PL 0/0:35:0:35:0,0,695 -20_10037292_10066351 8905 . A . . END=8905 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 8906 . G . . END=8906 GT:DP:GQ:MIN_DP:PL 0/0:35:0:35:0,0,689 -20_10037292_10066351 8907 . A . . END=8907 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8908 . G . . END=8908 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1032 -20_10037292_10066351 8909 . A . . END=8911 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8912 . G . . END=8912 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,963 -20_10037292_10066351 8913 . A . . END=8916 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 8917 . A . . END=8917 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,870 -20_10037292_10066351 8918 . G . . END=8918 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,892 -20_10037292_10066351 8919 . A . . END=8919 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 8920 . A . . END=8920 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,867 -20_10037292_10066351 8921 . A . . END=8921 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8922 . G . . END=8922 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,925 -20_10037292_10066351 8923 . A . . END=8923 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 8924 . G . . END=8924 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,884 -20_10037292_10066351 8925 . G . . END=8925 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,925 -20_10037292_10066351 8926 . A . . END=8926 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,827 -20_10037292_10066351 8927 . A . . END=8928 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 8929 . G . . END=8929 GT:DP:GQ:MIN_DP:PL 0/0:32:33:32:0,33,853 -20_10037292_10066351 8930 . A . . END=8931 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,1215 -20_10037292_10066351 8932 . A . . END=8932 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8933 . G . . END=8933 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,979 -20_10037292_10066351 8934 . A . . END=8937 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 8938 . A . . END=8938 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,1170 -20_10037292_10066351 8939 . G . . END=8939 GT:DP:GQ:MIN_DP:PL 0/0:35:42:35:0,42,927 -20_10037292_10066351 8940 . A . . END=8941 GT:DP:GQ:MIN_DP:PL 0/0:34:81:32:0,81,1215 -20_10037292_10066351 8942 . A . . END=8944 GT:DP:GQ:MIN_DP:PL 0/0:34:78:33:0,78,1170 -20_10037292_10066351 8945 . G . . END=8945 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,909 -20_10037292_10066351 8946 . A . . END=8948 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,882 -20_10037292_10066351 8949 . G . . END=8952 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 -20_10037292_10066351 8953 . G . . END=8953 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,878 -20_10037292_10066351 8954 . A . . END=8954 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8955 . G . . END=8955 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,881 -20_10037292_10066351 8956 . A . . END=8961 GT:DP:GQ:MIN_DP:PL 0/0:32:80:30:0,80,916 -20_10037292_10066351 8962 . A . . END=8963 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,869 -20_10037292_10066351 8964 . A . . END=8964 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8965 . G . . END=8965 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,792 -20_10037292_10066351 8966 . A . . END=8967 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,872 -20_10037292_10066351 8968 . G . . END=8968 GT:DP:GQ:MIN_DP:PL 0/0:33:27:33:0,27,752 -20_10037292_10066351 8969 . G . . END=8974 GT:DP:GQ:MIN_DP:PL 0/0:34:83:32:0,83,944 -20_10037292_10066351 8975 . G . . END=8975 GT:DP:GQ:MIN_DP:PL 0/0:34:70:34:0,70,857 -20_10037292_10066351 8976 . A . . END=8976 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1260 -20_10037292_10066351 8977 . G . . END=8977 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,895 -20_10037292_10066351 8978 . A . . END=8980 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 8981 . G . . END=8981 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,921 -20_10037292_10066351 8982 . A . . END=8984 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8985 . A . . END=8993 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 8994 . A . . END=8994 GT:DP:GQ:MIN_DP:PL 0/0:31:68:31:0,68,872 -20_10037292_10066351 8995 . G . . END=8995 GT:DP:GQ:MIN_DP:PL 0/0:31:28:31:0,28,772 -20_10037292_10066351 8996 . A . . END=8996 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8997 . G . . END=8997 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,833 -20_10037292_10066351 8998 . A . . END=9007 GT:DP:GQ:MIN_DP:PL 0/0:33:81:30:0,81,958 -20_10037292_10066351 9008 . G . . END=9008 GT:DP:GQ:MIN_DP:PL 0/0:34:73:34:0,73,965 -20_10037292_10066351 9009 . A . . END=9010 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 9011 . G . . END=9011 GT:DP:GQ:MIN_DP:PL 0/0:34:66:34:0,66,929 -20_10037292_10066351 9012 . G . . END=9013 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,908 -20_10037292_10066351 9014 . A . . END=9014 GT:DP:GQ:MIN_DP:PL 0/0:33:70:33:0,70,956 -20_10037292_10066351 9015 . G . . END=9015 GT:DP:GQ:MIN_DP:PL 0/0:32:13:32:0,13,731 -20_10037292_10066351 9016 . G . . END=9016 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,884 -20_10037292_10066351 9017 . A . . END=9017 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1007 -20_10037292_10066351 9018 . A . . END=9018 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9019 . G . . END=9019 GT:DP:GQ:MIN_DP:PL 0/0:39:69:39:0,69,1010 -20_10037292_10066351 9020 . A . . END=9020 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 9021 . A . . END=9021 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1070 -20_10037292_10066351 9022 . A . . END=9024 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1080 -20_10037292_10066351 9025 . T . . END=9025 GT:DP:GQ:MIN_DP:PL 0/0:37:0:37:0,0,654 -20_10037292_10066351 9026 . G . . END=9026 GT:DP:GQ:MIN_DP:PL 0/0:37:83:37:0,83,1047 -20_10037292_10066351 9027 . A . . END=9028 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1620 -20_10037292_10066351 9029 . G . . END=9029 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1046 -20_10037292_10066351 9030 . G . . END=9030 GT:DP:GQ:MIN_DP:PL 0/0:38:56:38:0,56,999 -20_10037292_10066351 9031 . G . . END=9031 GT:DP:GQ:MIN_DP:PL 0/0:38:70:38:0,70,1004 -20_10037292_10066351 9032 . A . . END=9032 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9033 . G . . END=9033 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1083 -20_10037292_10066351 9034 . G . . END=9034 GT:DP:GQ:MIN_DP:PL 0/0:38:25:38:0,25,908 -20_10037292_10066351 9035 . A . . END=9035 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1012 -20_10037292_10066351 9036 . A . . END=9036 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9037 . G . . END=9037 GT:DP:GQ:MIN_DP:PL 0/0:38:71:38:0,71,1040 -20_10037292_10066351 9038 . G . . END=9038 GT:DP:GQ:MIN_DP:PL 0/0:36:41:36:0,41,937 -20_10037292_10066351 9039 . A . . END=9042 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 9043 . A . . END=9043 GT:DP:GQ:MIN_DP:PL 0/0:36:83:36:0,83,1090 -20_10037292_10066351 9044 . G . . END=9044 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 9045 . G . . END=9045 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1010 -20_10037292_10066351 9046 . A . . END=9050 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 9051 . G . . END=9051 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,1041 -20_10037292_10066351 9052 . G . . END=9052 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1030 -20_10037292_10066351 9053 . A . . END=9053 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 9054 . A . . END=9054 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,1075 -20_10037292_10066351 9055 . G . . END=9060 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,101,974 -20_10037292_10066351 9061 . A . . END=9068 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 9069 . G . . END=9069 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1056 -20_10037292_10066351 9070 . A . . END=9070 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 9071 . A . . END=9071 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 9072 . G . . END=9073 GT:DP:GQ:MIN_DP:PL 0/0:37:64:37:0,64,1071 -20_10037292_10066351 9074 . A . . END=9074 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9075 . A . . END=9076 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,106,1209 -20_10037292_10066351 9077 . A . . END=9082 GT:DP:GQ:MIN_DP:PL 0/0:38:90:36:0,90,1214 -20_10037292_10066351 9083 . G . . END=9083 GT:DP:GQ:MIN_DP:PL 0/0:37:86:37:0,86,1135 -20_10037292_10066351 9084 . G . . END=9084 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 9085 . G . . END=9085 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1148 -20_10037292_10066351 9086 . G . . END=9088 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 9089 . G . . END=9097 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,934 -20_10037292_10066351 9098 . G . . END=9098 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,971 -20_10037292_10066351 9099 . G . . END=9101 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,981 -20_10037292_10066351 9102 . T . . END=9102 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,847 -20_10037292_10066351 9103 . A . . END=9103 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,860 -20_10037292_10066351 9104 . A . . END=9104 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 9105 . A . . END=9105 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 9106 . G . . END=9106 GT:DP:GQ:MIN_DP:PL 0/0:29:64:29:0,64,878 -20_10037292_10066351 9107 . A . . END=9107 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 9108 . A . . END=9108 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9109 . A . . END=9109 GT:DP:GQ:MIN_DP:PL 0/0:31:71:31:0,71,936 -20_10037292_10066351 9110 . G . . END=9110 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,914 -20_10037292_10066351 9111 . A . . END=9112 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9113 . G . . END=9118 GT:DP:GQ:MIN_DP:PL 0/0:31:72:31:0,72,1080 -20_10037292_10066351 9119 . G . . END=9119 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,873 -20_10037292_10066351 9120 . A . . END=9120 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 9121 . T . . END=9121 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,869 -20_10037292_10066351 9122 . G . . END=9122 GT:DP:GQ:MIN_DP:PL 0/0:28:52:28:0,52,788 -20_10037292_10066351 9123 . G . . END=9123 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,830 -20_10037292_10066351 9124 . A . . END=9124 GT:DP:GQ:MIN_DP:PL 0/0:28:51:28:0,51,802 -20_10037292_10066351 9125 . G . . END=9125 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,799 -20_10037292_10066351 9126 . A . . END=9126 GT:DP:GQ:MIN_DP:PL 0/0:27:58:27:0,58,789 -20_10037292_10066351 9127 . A . . END=9127 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 9128 . G . . END=9128 GT:DP:GQ:MIN_DP:PL 0/0:27:53:27:0,53,781 -20_10037292_10066351 9129 . A . . END=9135 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,809 -20_10037292_10066351 9136 . A . . END=9136 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,796 -20_10037292_10066351 9137 . C . . END=9140 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 9141 . A . . END=9142 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 9143 . A . . END=9143 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,887 -20_10037292_10066351 9144 . A . . END=9145 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9146 . T . . END=9146 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,817 -20_10037292_10066351 9147 . G . . END=9147 GT:DP:GQ:MIN_DP:PL 0/0:29:69:29:0,69,824 -20_10037292_10066351 9148 . G . . END=9148 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,800 -20_10037292_10066351 9149 . C . . END=9152 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,822 -20_10037292_10066351 9153 . T . . END=9153 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,914 -20_10037292_10066351 9154 . A . . END=9154 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,804 -20_10037292_10066351 9155 . C . . END=9158 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,889 -20_10037292_10066351 9159 . C . . END=9163 GT:DP:GQ:MIN_DP:PL 0/0:34:81:27:0,81,827 -20_10037292_10066351 9164 . C . . END=9167 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1016 -20_10037292_10066351 9168 . A . . END=9168 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 9169 . C . . END=9175 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9176 . A . . END=9199 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,981 -20_10037292_10066351 9200 . T . . END=9200 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1180 -20_10037292_10066351 9201 . T . . END=9201 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,111,1221 -20_10037292_10066351 9202 . T . . END=9202 GT:DP:GQ:MIN_DP:PL 0/0:42:90:42:0,90,1135 -20_10037292_10066351 9203 . C . . END=9225 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,100,1080 -20_10037292_10066351 9226 . G . . END=9226 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1056 -20_10037292_10066351 9227 . C . . END=9227 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9228 . T . . END=9228 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1056 -20_10037292_10066351 9229 . C . . END=9229 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 9230 . T . . END=9230 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1055 -20_10037292_10066351 9231 . C . . END=9236 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,104,1030 -20_10037292_10066351 9237 . G . . END=9237 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1042 -20_10037292_10066351 9238 . C . . END=9239 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1017 -20_10037292_10066351 9240 . A . . END=9242 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 9243 . T . . END=9244 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1084 -20_10037292_10066351 9245 . A G, 26.64 . BaseQRankSum=-1.133;DP=35;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=126000,35;ReadPosRankSum=1.071 GT:AD:DP:GQ:PL:SB 0/1:29,5,0:34:34:34,0,814,120,828,948:11,18,1,4 -20_10037292_10066351 9246 . T . . END=9246 GT:DP:GQ:MIN_DP:PL 0/0:37:83:37:0,83,1071 -20_10037292_10066351 9247 . T . . END=9262 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1084 -20_10037292_10066351 9263 . G . . END=9265 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1018 -20_10037292_10066351 9266 . T . . END=9266 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,111,1161 -20_10037292_10066351 9267 . G . . END=9267 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1120 -20_10037292_10066351 9268 . A . . END=9268 GT:DP:GQ:MIN_DP:PL 0/0:38:73:38:0,73,909 -20_10037292_10066351 9269 . C . . END=9350 GT:DP:GQ:MIN_DP:PL 0/0:45:99:38:0,105,1281 -20_10037292_10066351 9351 . A . . END=9351 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1158 -20_10037292_10066351 9352 . T . . END=9355 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,105,1575 -20_10037292_10066351 9356 . C . . END=9356 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1127 -20_10037292_10066351 9357 . A . . END=9358 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1169 -20_10037292_10066351 9359 . A . . END=9359 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1110 -20_10037292_10066351 9360 . C . . END=9361 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1087 -20_10037292_10066351 9362 . C . . END=9362 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1186 -20_10037292_10066351 9363 . T . . END=9406 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,104,1220 -20_10037292_10066351 9407 . G . . END=9407 GT:DP:GQ:MIN_DP:PL 0/0:45:93:45:0,93,1366 -20_10037292_10066351 9408 . C . . END=9414 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,105,1575 -20_10037292_10066351 9415 . T . . END=9425 GT:DP:GQ:MIN_DP:PL 0/0:39:90:35:0,90,1068 -20_10037292_10066351 9426 . T . . END=9427 GT:DP:GQ:MIN_DP:PL 0/0:33:81:32:0,81,996 -20_10037292_10066351 9428 . A . . END=9428 GT:DP:GQ:MIN_DP:PL 0/0:32:71:32:0,71,957 -20_10037292_10066351 9429 . C . . END=9439 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,877 -20_10037292_10066351 9440 . T . . END=9440 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9441 . T . . END=9452 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,1215 -20_10037292_10066351 9453 . A . . END=9454 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,870 -20_10037292_10066351 9455 . G . . END=9457 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 9458 . A . . END=9468 GT:DP:GQ:MIN_DP:PL 0/0:30:72:29:0,72,898 -20_10037292_10066351 9469 . T . . END=9469 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,791 -20_10037292_10066351 9470 . C . . END=9471 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 9472 . G . . END=9488 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,965 -20_10037292_10066351 9489 . C . . END=9489 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,962 -20_10037292_10066351 9490 . C . . END=9491 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,946 -20_10037292_10066351 9492 . A . . END=9493 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,1034 -20_10037292_10066351 9494 . A . . END=9494 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1040 -20_10037292_10066351 9495 . T . . END=9495 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9496 . A . . END=9496 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 9497 . T . . END=9497 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1047 -20_10037292_10066351 9498 . C . . END=9500 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 9501 . C . . END=9505 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9506 . C . . END=9507 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 9508 . T . . END=9508 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9509 . G . . END=9512 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,1305 -20_10037292_10066351 9513 . C . . END=9513 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 9514 . C . . END=9518 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 9519 . G . . END=9519 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,915 -20_10037292_10066351 9520 . C . . END=9521 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9522 . C . . END=9525 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 9526 . C . . END=9528 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 9529 . A . . END=9529 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,772 -20_10037292_10066351 9530 . C . . END=9533 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 9534 . A . . END=9534 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,826 -20_10037292_10066351 9535 . A . . END=9544 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9545 . A . . END=9546 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,800 -20_10037292_10066351 9547 . T . . END=9549 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,954 -20_10037292_10066351 9550 . A . . END=9551 GT:DP:GQ:MIN_DP:PL 0/0:32:70:31:0,70,887 -20_10037292_10066351 9552 . C . . END=9552 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 9553 . T . . END=9553 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,925 -20_10037292_10066351 9554 . C . . END=9556 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9557 . A . . END=9558 GT:DP:GQ:MIN_DP:PL 0/0:31:72:30:0,72,839 -20_10037292_10066351 9559 . A . . END=9562 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,959 -20_10037292_10066351 9563 . T . . END=9563 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,1004 -20_10037292_10066351 9564 . T . . END=9564 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1041 -20_10037292_10066351 9565 . G . . END=9565 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,927 -20_10037292_10066351 9566 . T . . END=9567 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9568 . A . . END=9568 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,887 -20_10037292_10066351 9569 . C . . END=9569 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9570 . T . . END=9570 GT:DP:GQ:MIN_DP:PL 0/0:33:54:33:0,54,838 -20_10037292_10066351 9571 . C . . END=9571 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9572 . T . . END=9572 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,963 -20_10037292_10066351 9573 . T . . END=9574 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9575 . C . . END=9575 GT:DP:GQ:MIN_DP:PL 0/0:33:88:33:0,88,1021 -20_10037292_10066351 9576 . T . . END=9576 GT:DP:GQ:MIN_DP:PL 0/0:34:54:34:0,54,906 -20_10037292_10066351 9577 . C . . END=9578 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9579 . T . . END=9579 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,994 -20_10037292_10066351 9580 . A . . END=9580 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,872 -20_10037292_10066351 9581 . C . . END=9587 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 9588 . C . . END=9589 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,862 -20_10037292_10066351 9590 . C . . END=9593 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9594 . T . . END=9607 GT:DP:GQ:MIN_DP:PL 0/0:38:99:34:0,99,956 -20_10037292_10066351 9608 . A . . END=9608 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1158 -20_10037292_10066351 9609 . C . . END=9646 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,107,1228 -20_10037292_10066351 9647 . G . . END=9647 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1214 -20_10037292_10066351 9648 . A . . END=9650 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,114,1710 -20_10037292_10066351 9651 . T . . END=9651 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1301 -20_10037292_10066351 9652 . G . . END=9659 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,114,1710 -20_10037292_10066351 9660 . A . . END=9660 GT:DP:GQ:MIN_DP:PL 0/0:40:98:40:0,98,1230 -20_10037292_10066351 9661 . T . . END=9687 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,102,1188 -20_10037292_10066351 9688 . A . . END=9688 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1182 -20_10037292_10066351 9689 . C . . END=9700 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,117,1755 -20_10037292_10066351 9701 . A . . END=9701 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1221 -20_10037292_10066351 9702 . C . . END=9711 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,107,1235 -20_10037292_10066351 9712 . C . . END=9712 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1180 -20_10037292_10066351 9713 . A . . END=9736 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1195 -20_10037292_10066351 9737 . T . . END=9745 GT:DP:GQ:MIN_DP:PL 0/0:39:90:37:0,90,1350 -20_10037292_10066351 9746 . T . . END=9748 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 9749 . C . . END=9753 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 9754 . A . . END=9754 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,887 -20_10037292_10066351 9755 . A . . END=9755 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 9756 . T . . END=9757 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 9758 . A . . END=9758 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 9759 . A . . END=9761 GT:DP:GQ:MIN_DP:PL 0/0:33:84:32:0,84,1260 -20_10037292_10066351 9762 . T . . END=9762 GT:DP:GQ:MIN_DP:PL 0/0:34:78:34:0,78,1064 -20_10037292_10066351 9763 . A . . END=9765 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9766 . T . . END=9770 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1058 -20_10037292_10066351 9771 . A . . END=9771 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9772 . A . . END=9772 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1019 -20_10037292_10066351 9773 . T . . END=9775 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 9776 . C . . END=9777 GT:DP:GQ:MIN_DP:PL 0/0:36:77:35:0,77,1058 -20_10037292_10066351 9778 . G . . END=9781 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 -20_10037292_10066351 9782 . T . . END=9782 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,948 -20_10037292_10066351 9783 . T . . END=9783 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9784 . C . . END=9784 GT:DP:GQ:MIN_DP:PL 0/0:31:66:31:0,66,973 -20_10037292_10066351 9785 . T . . END=9787 GT:DP:GQ:MIN_DP:PL 0/0:31:86:30:0,86,975 -20_10037292_10066351 9788 . A . . END=9789 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9790 . A . . END=9792 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,955 -20_10037292_10066351 9793 . A . . END=9793 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 9794 . T . . END=9794 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 9795 . A . . END=9796 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1015 -20_10037292_10066351 9797 . G . . END=9797 GT:DP:GQ:MIN_DP:PL 0/0:35:64:35:0,64,953 -20_10037292_10066351 9798 . A . . END=9801 GT:DP:GQ:MIN_DP:PL 0/0:36:91:35:0,91,1068 -20_10037292_10066351 9802 . T . . END=9809 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 9810 . A . . END=9810 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1101 -20_10037292_10066351 9811 . A . . END=9818 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 9819 . T . . END=9820 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1112 -20_10037292_10066351 9821 . T . . END=9830 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 9831 . A . . END=9831 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1115 -20_10037292_10066351 9832 . G . . END=9848 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,99,1122 -20_10037292_10066351 9849 . A . . END=9849 GT:DP:GQ:MIN_DP:PL 0/0:38:87:38:0,87,1030 -20_10037292_10066351 9850 . C . . END=9851 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1173 -20_10037292_10066351 9852 . C . . END=9852 GT:DP:GQ:MIN_DP:PL 0/0:37:52:37:0,52,971 -20_10037292_10066351 9853 . C . . END=9855 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1135 -20_10037292_10066351 9856 . C . . END=9856 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1125 -20_10037292_10066351 9857 . C . . END=9859 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1530 -20_10037292_10066351 12912 . G . . END=12912 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1203 -20_10037292_10066351 12913 . A . . END=12913 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 12914 . G . . END=12914 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1239 -20_10037292_10066351 12915 . C . . END=12935 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1157 -20_10037292_10066351 12936 . T . . END=12936 GT:DP:GQ:MIN_DP:PL 0/0:41:76:41:0,76,1212 -20_10037292_10066351 12937 . T . . END=12942 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,105,1575 -20_10037292_10066351 12943 . A . . END=12943 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1236 -20_10037292_10066351 12944 . A . . END=12978 GT:DP:GQ:MIN_DP:PL 0/0:41:99:36:0,105,1107 -20_10037292_10066351 12979 . A . . END=12979 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1213 -20_10037292_10066351 12980 . G . . END=12983 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1193 -20_10037292_10066351 12984 . G . . END=12984 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1260 -20_10037292_10066351 12985 . A . . END=13012 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,102,1146 -20_10037292_10066351 13013 . A . . END=13013 GT:DP:GQ:MIN_DP:PL 0/0:41:92:41:0,92,1181 -20_10037292_10066351 13014 . A . . END=13016 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1138 -20_10037292_10066351 13017 . C . . END=13017 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1020 -20_10037292_10066351 13018 . G . . END=13023 GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,105,1575 -20_10037292_10066351 13024 . A . . END=13024 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,1028 -20_10037292_10066351 13025 . A . . END=13028 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,101,1192 -20_10037292_10066351 13029 . T . . END=13029 GT:DP:GQ:MIN_DP:PL 0/0:42:86:42:0,86,1160 -20_10037292_10066351 13030 . A . . END=13032 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,108,1620 -20_10037292_10066351 13033 . G . . END=13033 GT:DP:GQ:MIN_DP:PL 0/0:42:81:42:0,81,1210 -20_10037292_10066351 13034 . A . . END=13034 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1575 -20_10037292_10066351 13035 . G . . END=13035 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1181 -20_10037292_10066351 13036 . T . . END=13054 GT:DP:GQ:MIN_DP:PL 0/0:40:99:36:0,99,1182 -20_10037292_10066351 13055 . T . . END=13055 GT:DP:GQ:MIN_DP:PL 0/0:36:97:36:0,97,1060 -20_10037292_10066351 13056 . C . . END=13057 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1145 -20_10037292_10066351 13058 . A . . END=13058 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1067 -20_10037292_10066351 13059 . T . . END=13060 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1124 -20_10037292_10066351 13061 . G . . END=13061 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1045 -20_10037292_10066351 13062 . G . . END=13062 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,107,1074 -20_10037292_10066351 13063 . T . . END=13063 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1106 -20_10037292_10066351 13064 . T . . END=13070 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,108,1620 -20_10037292_10066351 13071 . T . . END=13071 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1199 -20_10037292_10066351 13072 . T . . END=13078 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,104,1206 -20_10037292_10066351 13079 . A . . END=13079 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1440 -20_10037292_10066351 13080 . G . . END=13082 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,99,1485 -20_10037292_10066351 13083 . T . . END=13083 GT:DP:GQ:MIN_DP:PL 0/0:40:92:40:0,92,1186 -20_10037292_10066351 13084 . C . . END=13090 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,102,1207 -20_10037292_10066351 13091 . G . . END=13091 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1168 -20_10037292_10066351 13092 . T . . END=13092 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1137 -20_10037292_10066351 13093 . G . . END=13175 GT:DP:GQ:MIN_DP:PL 0/0:47:99:38:0,106,1209 -20_10037292_10066351 13176 . C . . END=13176 GT:DP:GQ:MIN_DP:PL 0/0:45:76:45:0,76,1292 -20_10037292_10066351 13177 . T . . END=13203 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,101,1297 -20_10037292_10066351 13204 . G . . END=13204 GT:DP:GQ:MIN_DP:PL 0/0:46:89:46:0,89,1350 -20_10037292_10066351 13205 . T . . END=13220 GT:DP:GQ:MIN_DP:PL 0/0:46:99:41:0,109,1372 -20_10037292_10066351 13221 . T . . END=13221 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1139 -20_10037292_10066351 13222 . A . . END=13261 GT:DP:GQ:MIN_DP:PL 0/0:40:99:33:0,99,1021 -20_10037292_10066351 13262 . A . . END=13262 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1069 -20_10037292_10066351 13263 . A . . END=13266 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 13267 . G . . END=13269 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1215 -20_10037292_10066351 13270 . A . . END=13283 GT:DP:GQ:MIN_DP:PL 0/0:34:72:27:0,72,1080 -20_10037292_10066351 13284 . G . . END=13284 GT:DP:GQ:MIN_DP:PL 0/0:28:56:28:0,56,767 -20_10037292_10066351 13285 . C . . END=13287 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 13288 . G . . END=13288 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13289 . T . . END=13289 GT:DP:GQ:MIN_DP:PL 0/0:29:65:29:0,65,809 -20_10037292_10066351 13290 . C . . END=13294 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,828 -20_10037292_10066351 13295 . T . . END=13306 GT:DP:GQ:MIN_DP:PL 0/0:27:78:26:0,78,767 -20_10037292_10066351 13307 . T . . END=13309 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,798 -20_10037292_10066351 13310 . T . . END=13312 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,890 -20_10037292_10066351 13313 . T . . END=13314 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1026 -20_10037292_10066351 13315 . T . . END=13321 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1018 -20_10037292_10066351 13322 . C . . END=13329 GT:DP:GQ:MIN_DP:PL 0/0:33:81:30:0,81,1215 -20_10037292_10066351 13330 . C . . END=13330 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,958 -20_10037292_10066351 13331 . A . . END=13344 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 13345 . C . . END=13345 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13346 . T . . END=13348 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13349 . G . . END=13349 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13350 . A . . END=13352 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13353 . T . . END=13355 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13356 . C . . END=13356 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13357 . T . . END=13360 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13361 . A . . END=13371 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 13372 . A . . END=13372 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,873 -20_10037292_10066351 13373 . A . . END=13377 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13378 . T . . END=13378 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20_10037292_10066351 13379 . G . . END=13383 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 13384 . G . . END=13384 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,939 -20_10037292_10066351 13385 . T . . END=13392 GT:DP:GQ:MIN_DP:PL 0/0:31:81:29:0,81,987 -20_10037292_10066351 13393 . C . . END=13393 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13394 . A . . END=13395 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13396 . C . . END=13399 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 13400 . T . . END=13404 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13405 . T . . END=13405 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1033 -20_10037292_10066351 13406 . C . . END=13418 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1017 -20_10037292_10066351 13419 . G . . END=13419 GT:DP:GQ:MIN_DP:PL 0/0:35:86:35:0,86,1024 -20_10037292_10066351 13420 . C . . END=13428 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13429 . T . . END=13430 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1097 -20_10037292_10066351 13431 . G . . END=13433 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13434 . A . . END=13434 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1012 -20_10037292_10066351 13435 . A . . END=13438 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13439 . G . . END=13439 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,934 -20_10037292_10066351 13440 . T . . END=13440 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 13441 . T . . END=13441 GT:DP:GQ:MIN_DP:PL 0/0:35:92:35:0,92,996 -20_10037292_10066351 13442 . T . . END=13444 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 13445 . C . . END=13449 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,966 -20_10037292_10066351 13450 . C . . END=13451 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13452 . G . . END=13460 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1012 -20_10037292_10066351 13461 . T . . END=13461 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,987 -20_10037292_10066351 13462 . T . . END=13462 GT:DP:GQ:MIN_DP:PL 0/0:35:54:35:0,54,861 -20_10037292_10066351 13463 . C . . END=13463 GT:DP:GQ:MIN_DP:PL 0/0:33:32:33:0,32,865 -20_10037292_10066351 13464 . T . . END=13535 GT:DP:GQ:MIN_DP:PL 0/0:44:99:36:0,99,1095 -20_10037292_10066351 13536 . T C, 437.64 . BaseQRankSum=1.454;DP=45;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=162000,45;ReadPosRankSum=-1.613 GT:AD:DP:GQ:PL:SB 0/1:26,18,0:44:99:445,0,672,523,726,1249:15,11,11,7 -20_10037292_10066351 13537 . T . . END=13548 GT:DP:GQ:MIN_DP:PL 0/0:45:99:40:0,111,1665 -20_10037292_10066351 13549 . A . . END=13549 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1215 -20_10037292_10066351 13550 . G . . END=13554 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,100,1128 -20_10037292_10066351 13555 . A . . END=13556 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1079 -20_10037292_10066351 13557 . A . . END=13561 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 13562 . C . . END=13562 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1093 -20_10037292_10066351 13563 . T . . END=13563 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 13564 . G . . END=13564 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1104 -20_10037292_10066351 13565 . C . . END=13565 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 13566 . C . . END=13566 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1134 -20_10037292_10066351 13567 . C . . END=13577 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1146 -20_10037292_10066351 13578 . T . . END=13578 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1063 -20_10037292_10066351 13579 . A . . END=13579 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13580 . G . . END=13588 GT:DP:GQ:MIN_DP:PL 0/0:36:96:33:0,96,1440 -20_10037292_10066351 13589 . T . . END=13589 GT:DP:GQ:MIN_DP:PL 0/0:33:79:33:0,79,939 -20_10037292_10066351 13590 . G . . END=13590 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,991 -20_10037292_10066351 13591 . T . . END=13591 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,960 -20_10037292_10066351 13592 . C . . END=13592 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,966 -20_10037292_10066351 13593 . A . . END=13593 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 13594 . G . . END=13595 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,958 -20_10037292_10066351 13596 . T . . END=13596 GT:DP:GQ:MIN_DP:PL 0/0:35:75:35:0,75,994 -20_10037292_10066351 13597 . G . . END=13599 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13600 . T . . END=13603 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13604 . T . . END=13604 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1031 -20_10037292_10066351 13605 . C . . END=13605 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13606 . T . . END=13607 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 13608 . A . . END=13610 GT:DP:GQ:MIN_DP:PL 0/0:36:83:35:0,83,982 -20_10037292_10066351 13611 . A . . END=13617 GT:DP:GQ:MIN_DP:PL 0/0:36:90:33:0,90,1350 -20_10037292_10066351 13618 . T . . END=13631 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 13632 . A . . END=13632 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,941 -20_10037292_10066351 13633 . G . . END=13639 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13640 . C . . END=13640 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 13641 . A . . END=13654 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13655 . G . . END=13655 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,944 -20_10037292_10066351 13656 . C . . END=13657 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,980 -20_10037292_10066351 13658 . T . . END=13671 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,890 -20_10037292_10066351 13672 . T . . END=13684 GT:DP:GQ:MIN_DP:PL 0/0:34:83:32:0,83,982 -20_10037292_10066351 13685 . G . . END=13686 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13687 . A . . END=13687 GT:DP:GQ:MIN_DP:PL 0/0:30:69:30:0,69,896 -20_10037292_10066351 13688 . A . . END=13703 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,879 -20_10037292_10066351 13704 . C . . END=13704 GT:DP:GQ:MIN_DP:PL 0/0:33:52:33:0,52,943 -20_10037292_10066351 13705 . C . . END=13707 GT:DP:GQ:MIN_DP:PL 0/0:33:93:31:0,93,874 -20_10037292_10066351 13708 . C . . END=13708 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 13709 . C . . END=13709 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,983 -20_10037292_10066351 13710 . G . . END=13715 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1530 -20_10037292_10066351 13716 . T . . END=13716 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1076 -20_10037292_10066351 13717 . C . . END=13717 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 13718 . A . . END=13718 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1070 -20_10037292_10066351 13719 . G . . END=13726 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,102,1091 -20_10037292_10066351 13727 . A . . END=13727 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1125 -20_10037292_10066351 13728 . A . . END=13757 GT:DP:GQ:MIN_DP:PL 0/0:40:99:36:0,99,1146 -20_10037292_10066351 13758 . A . . END=13758 GT:DP:GQ:MIN_DP:PL 0/0:36:61:36:0,61,1017 -20_10037292_10066351 13759 . T . . END=13767 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1019 -20_10037292_10066351 13768 . T . . END=13768 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 13769 . G . . END=13771 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 13772 . T . . END=13776 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 13777 . A . . END=13778 GT:DP:GQ:MIN_DP:PL 0/0:35:87:34:0,87,1305 -20_10037292_10066351 13779 . C . . END=13779 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,969 -20_10037292_10066351 13780 . A . . END=13797 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 13798 . T . . END=13802 GT:DP:GQ:MIN_DP:PL 0/0:29:75:29:0,75,1125 -20_10037292_10066351 13803 . C . . END=13804 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 13805 . G . . END=13805 GT:DP:GQ:MIN_DP:PL 0/0:30:71:30:0,71,951 -20_10037292_10066351 13806 . C . . END=13807 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 13808 . T . . END=13815 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 13816 . A . . END=13840 GT:DP:GQ:MIN_DP:PL 0/0:30:80:27:0,80,850 -20_10037292_10066351 13841 . A . . END=13843 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13844 . A . . END=13847 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13848 . G . . END=13848 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13849 . T . . END=13859 GT:DP:GQ:MIN_DP:PL 0/0:31:74:28:0,74,918 -20_10037292_10066351 13860 . T . . END=13862 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,835 -20_10037292_10066351 13863 . T . . END=13873 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 13874 . T . . END=13880 GT:DP:GQ:MIN_DP:PL 0/0:28:69:27:0,69,845 -20_10037292_10066351 13881 . A . . END=13881 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 13882 . C . . END=13882 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,1035 -20_10037292_10066351 13883 . C . . END=13883 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,750 -20_10037292_10066351 13884 . T . . END=13899 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,722 -20_10037292_10066351 13900 . A . . END=13900 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,739 -20_10037292_10066351 13901 . T . . END=13901 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,766 -20_10037292_10066351 13902 . A . . END=13902 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 13903 . A . . END=13903 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,701 -20_10037292_10066351 13904 . A . . END=13905 GT:DP:GQ:MIN_DP:PL 0/0:24:66:24:0,66,990 -20_10037292_10066351 13906 . A . . END=13921 GT:DP:GQ:MIN_DP:PL 0/0:26:72:24:0,72,735 -20_10037292_10066351 13922 . G . . END=13922 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,737 -20_10037292_10066351 13923 . C . . END=13932 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,806 -20_10037292_10066351 13933 . T . . END=13933 GT:DP:GQ:MIN_DP:PL 0/0:26:52:26:0,52,811 -20_10037292_10066351 13934 . G . . END=13942 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 13943 . A . . END=13943 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13944 . C . . END=13946 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 13947 . G . . END=13948 GT:DP:GQ:MIN_DP:PL 0/0:28:67:28:0,67,785 -20_10037292_10066351 13949 . A . . END=13952 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 13953 . T . . END=13954 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 13955 . G . . END=13957 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 13958 . A . . END=13958 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,843 -20_10037292_10066351 13959 . C . . END=13961 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 13962 . C . . END=13962 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,774 -20_10037292_10066351 13963 . T . . END=13963 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 13964 . G . . END=13973 GT:DP:GQ:MIN_DP:PL 0/0:26:66:25:0,66,798 -20_10037292_10066351 13974 . A . . END=13974 GT:DP:GQ:MIN_DP:PL 0/0:25:59:25:0,59,721 -20_10037292_10066351 13975 . G . . END=13976 GT:DP:GQ:MIN_DP:PL 0/0:25:66:24:0,66,990 -20_10037292_10066351 13977 . C . . END=13977 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,723 -20_10037292_10066351 13978 . T . . END=13985 GT:DP:GQ:MIN_DP:PL 0/0:25:66:24:0,66,990 -20_10037292_10066351 13986 . G . . END=13988 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,1080 -20_10037292_10066351 13989 . T . . END=13991 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 -20_10037292_10066351 13992 . A . . END=13992 GT:DP:GQ:MIN_DP:PL 0/0:25:55:25:0,55,697 -20_10037292_10066351 13993 . A . . END=13993 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 13994 . T . . END=13994 GT:DP:GQ:MIN_DP:PL 0/0:25:62:25:0,62,748 -20_10037292_10066351 13995 . T . . END=14002 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,808 -20_10037292_10066351 14003 . A . . END=14003 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,742 -20_10037292_10066351 14004 . A . . END=14006 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 14007 . C . . END=14013 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 -20_10037292_10066351 14014 . G . . END=14020 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 14021 . G . . END=14024 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 14025 . C . . END=14034 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 14035 . A . . END=14041 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 14042 . G . . END=14044 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 14045 . G . . END=14046 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 14047 . A . . END=14049 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 14050 . G . . END=14051 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,933 -20_10037292_10066351 14052 . G . . END=14055 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 14056 . G . . END=14056 GT:DP:GQ:MIN_DP:PL 0/0:32:85:32:0,85,933 -20_10037292_10066351 14057 . T . . END=14061 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,938 -20_10037292_10066351 14062 . A . . END=14062 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,925 -20_10037292_10066351 14063 . G . . END=14064 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,876 -20_10037292_10066351 14065 . T . . END=14065 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,778 -20_10037292_10066351 14066 . G . . END=14070 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 14071 . A . . END=14084 GT:DP:GQ:MIN_DP:PL 0/0:28:72:26:0,72,1080 -20_10037292_10066351 14085 . C . . END=14085 GT:DP:GQ:MIN_DP:PL 0/0:27:51:27:0,51,814 -20_10037292_10066351 14086 . C . . END=14086 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,791 -20_10037292_10066351 14087 . A . . END=14087 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 14088 . G . . END=14088 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,809 -20_10037292_10066351 14089 . C . . END=14095 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,796 -20_10037292_10066351 14096 . G . . END=14101 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 14102 . T . . END=14102 GT:DP:GQ:MIN_DP:PL 0/0:28:55:28:0,55,788 -20_10037292_10066351 14103 . C . . END=14112 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,879 -20_10037292_10066351 14113 . A . . END=14122 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,1080 -20_10037292_10066351 14123 . G . . END=14123 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,865 -20_10037292_10066351 14124 . C . . END=14129 GT:DP:GQ:MIN_DP:PL 0/0:27:72:24:0,72,686 -20_10037292_10066351 14130 . A . . END=14139 GT:DP:GQ:MIN_DP:PL 0/0:25:60:23:0,60,900 -20_10037292_10066351 14140 . A . . END=14141 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 -20_10037292_10066351 14142 . C . . END=14144 GT:DP:GQ:MIN_DP:PL 0/0:22:54:21:0,54,810 -20_10037292_10066351 14145 . T . . END=14146 GT:DP:GQ:MIN_DP:PL 0/0:21:51:21:0,51,765 -20_10037292_10066351 14147 . A . . END=14150 GT:DP:GQ:MIN_DP:PL 0/0:22:54:21:0,54,810 -20_10037292_10066351 14151 . T . . END=14154 GT:DP:GQ:MIN_DP:PL 0/0:20:51:19:0,51,765 -20_10037292_10066351 14155 . T . . END=14155 GT:DP:GQ:MIN_DP:PL 0/0:21:50:21:0,50,612 -20_10037292_10066351 14156 . T C, 183.64 . BaseQRankSum=0.703;DP=20;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=72000,20;ReadPosRankSum=-0.193 GT:AD:DP:GQ:PL:SB 0/1:12,8,0:20:99:191,0,319,227,343,570:5,7,5,3 -20_10037292_10066351 14157 . T . . END=14158 GT:DP:GQ:MIN_DP:PL 0/0:21:51:20:0,51,765 -20_10037292_10066351 14159 . T . . END=14159 GT:DP:GQ:MIN_DP:PL 0/0:20:48:20:0,48,720 -20_10037292_10066351 14160 . C . . END=14160 GT:DP:GQ:MIN_DP:PL 0/0:20:46:20:0,46,579 -20_10037292_10066351 14161 . C . . END=14161 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 -20_10037292_10066351 14162 . C . . END=14162 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 -20_10037292_10066351 14163 . C . . END=14164 GT:DP:GQ:MIN_DP:PL 0/0:22:57:22:0,57,855 -20_10037292_10066351 14165 . T . . END=14169 GT:DP:GQ:MIN_DP:PL 0/0:22:60:21:0,60,900 -20_10037292_10066351 14170 . C . . END=14170 GT:DP:GQ:MIN_DP:PL 0/0:22:48:22:0,48,666 -20_10037292_10066351 14171 . A . . END=14172 GT:DP:GQ:MIN_DP:PL 0/0:22:63:22:0,63,945 -20_10037292_10066351 14173 . T . . END=14173 GT:DP:GQ:MIN_DP:PL 0/0:24:55:24:0,55,714 -20_10037292_10066351 14174 . C . . END=14174 GT:DP:GQ:MIN_DP:PL 0/0:25:61:25:0,61,767 -20_10037292_10066351 14175 . A . . END=14176 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,785 -20_10037292_10066351 14177 . C . . END=14178 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,792 -20_10037292_10066351 14179 . C . . END=14187 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,778 -20_10037292_10066351 14188 . C . . END=14188 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 14189 . C . . END=14192 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 14193 . T . . END=14197 GT:DP:GQ:MIN_DP:PL 0/0:25:60:25:0,60,715 -20_10037292_10066351 14198 . A . . END=14209 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,750 -20_10037292_10066351 14210 . A . . END=14211 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,824 -20_10037292_10066351 14212 . G . . END=14212 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,802 -20_10037292_10066351 14213 . G . . END=14214 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 14215 . G . . END=14217 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,933 -20_10037292_10066351 14218 . T . . END=14218 GT:DP:GQ:MIN_DP:PL 0/0:31:76:31:0,76,874 -20_10037292_10066351 14219 . T . . END=14219 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,972 -20_10037292_10066351 14220 . G . . END=14220 GT:DP:GQ:MIN_DP:PL 0/0:31:75:31:0,75,937 -20_10037292_10066351 14221 . G . . END=14222 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,936 -20_10037292_10066351 14223 . T . . END=14224 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1004 -20_10037292_10066351 14225 . G . . END=14228 GT:DP:GQ:MIN_DP:PL 0/0:33:93:31:0,93,930 -20_10037292_10066351 14229 . C . . END=14230 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,102,1530 -20_10037292_10066351 14231 . T . . END=14232 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14233 . C . . END=14233 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1043 -20_10037292_10066351 14234 . A . . END=14235 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 14236 . G . . END=14236 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1041 -20_10037292_10066351 14237 . A . . END=14237 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 14238 . T . . END=14238 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1030 -20_10037292_10066351 14239 . T . . END=14239 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 14240 . T . . END=14247 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1077 -20_10037292_10066351 14248 . G . . END=14248 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1046 -20_10037292_10066351 14249 . A . . END=14249 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,949 -20_10037292_10066351 14250 . T . . END=14250 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1084 -20_10037292_10066351 14251 . T . . END=14251 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1020 -20_10037292_10066351 14252 . T . . END=14406 GT:DP:GQ:MIN_DP:PL 0/0:48:99:37:0,109,1169 -20_10037292_10066351 14407 . C . . END=14407 GT:DP:GQ:MIN_DP:PL 0/0:52:84:52:0,84,1360 -20_10037292_10066351 14408 . T . . END=14510 GT:DP:GQ:MIN_DP:PL 0/0:53:99:46:0,118,1386 -20_10037292_10066351 14511 . G . . END=14511 GT:DP:GQ:MIN_DP:PL 0/0:47:95:47:0,95,1387 -20_10037292_10066351 14512 . T . . END=14557 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,102,1196 -20_10037292_10066351 14558 . C . . END=14558 GT:DP:GQ:MIN_DP:PL 0/0:36:77:36:0,77,1030 -20_10037292_10066351 14559 . C . . END=14563 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1157 -20_10037292_10066351 14564 . A . . END=14565 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 14566 . T . . END=14566 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 14567 . G . . END=14571 GT:DP:GQ:MIN_DP:PL 0/0:38:93:37:0,93,1145 -20_10037292_10066351 14572 . T . . END=14573 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 14574 . A . . END=14576 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 14577 . G . . END=14577 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1065 -20_10037292_10066351 14578 . T . . END=14578 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 14579 . G . . END=14579 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1029 -20_10037292_10066351 14580 . C . . END=14581 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 14582 . C . . END=14583 GT:DP:GQ:MIN_DP:PL 0/0:33:73:33:0,73,985 -20_10037292_10066351 14584 . C . . END=14586 GT:DP:GQ:MIN_DP:PL 0/0:35:81:34:0,81,1215 -20_10037292_10066351 14587 . A . . END=14589 GT:DP:GQ:MIN_DP:PL 0/0:35:78:34:0,78,1170 -20_10037292_10066351 14590 . T . . END=14590 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1035 -20_10037292_10066351 14591 . A . . END=14597 GT:DP:GQ:MIN_DP:PL 0/0:35:72:27:0,72,1024 -20_10037292_10066351 14598 . T . . END=14598 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,836 -20_10037292_10066351 14599 . A . . END=14601 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,854 -20_10037292_10066351 14602 . G . . END=14603 GT:DP:GQ:MIN_DP:PL 0/0:27:63:26:0,63,794 -20_10037292_10066351 14604 . C . . END=14612 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,1080 -20_10037292_10066351 14613 . T . . END=14613 GT:DP:GQ:MIN_DP:PL 0/0:26:60:26:0,60,803 -20_10037292_10066351 14614 . A . . END=14617 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,822 -20_10037292_10066351 14618 . A . . END=14619 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 14620 . T . . END=14620 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,845 -20_10037292_10066351 14621 . C . . END=14626 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 14627 . T . . END=14627 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,946 -20_10037292_10066351 14628 . T . . END=14629 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,980 -20_10037292_10066351 14630 . A . . END=14634 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 14635 . A . . END=14636 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 14637 . A . . END=14649 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 14650 . T . . END=14653 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 14654 . A . . END=14656 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 14657 . T . . END=14657 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1040 -20_10037292_10066351 14658 . C . . END=14671 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 14672 . T . . END=14672 GT:DP:GQ:MIN_DP:PL 0/0:31:64:31:0,64,910 -20_10037292_10066351 14673 . T . . END=14673 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,1002 -20_10037292_10066351 14674 . G . . END=14674 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,839 -20_10037292_10066351 14675 . A . . END=14680 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,950 -20_10037292_10066351 14681 . A . . END=14681 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1051 -20_10037292_10066351 14682 . T . . END=14682 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,979 -20_10037292_10066351 14683 . C . . END=14683 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 14684 . T . . END=14684 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1045 -20_10037292_10066351 14685 . T . . END=14685 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 14686 . A . . END=14686 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,1047 -20_10037292_10066351 14687 . A . . END=14689 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14690 . G . . END=14690 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,961 -20_10037292_10066351 14691 . T . . END=14691 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 14692 . T . . END=14692 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1090 -20_10037292_10066351 14693 . T . . END=14694 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 14695 . A . . END=14695 GT:DP:GQ:MIN_DP:PL 0/0:35:62:35:0,62,1010 -20_10037292_10066351 14696 . A . . END=14696 GT:DP:GQ:MIN_DP:PL 0/0:38:88:38:0,88,1135 -20_10037292_10066351 14697 . A . . END=14698 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 14699 . T . . END=14699 GT:DP:GQ:MIN_DP:PL 0/0:38:55:38:0,55,1027 -20_10037292_10066351 14700 . A . . END=14703 GT:DP:GQ:MIN_DP:PL 0/0:37:91:37:0,91,1149 -20_10037292_10066351 14704 . A . . END=14704 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1106 -20_10037292_10066351 14705 . A . . END=14706 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1193 -20_10037292_10066351 14707 . A . . END=14707 GT:DP:GQ:MIN_DP:PL 0/0:37:64:37:0,64,1029 -20_10037292_10066351 14708 . A . . END=14709 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 14710 . T . . END=14712 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 14713 . T . . END=14713 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1128 -20_10037292_10066351 14714 . T . . END=14718 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1192 -20_10037292_10066351 14719 . T . . END=14719 GT:DP:GQ:MIN_DP:PL 0/0:36:82:36:0,82,1087 -20_10037292_10066351 14720 . T . . END=14737 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,100,1160 diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf.idx b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf.idx deleted file mode 100644 index 63861603f..000000000 Binary files a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf.idx and /dev/null differ diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf deleted file mode 100644 index 63eccf733..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf +++ /dev/null @@ -1,1672 +0,0 @@ -##fileformat=VCFv4.2 -##ALT= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= 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G . . END=3282 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,719 -20_10037292_10066351 3283 . T . . END=3283 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,833 -20_10037292_10066351 3284 . T . . END=3287 GT:DP:GQ:MIN_DP:PL 0/0:29:78:27:0,78,1170 -20_10037292_10066351 3288 . A . . END=3290 GT:DP:GQ:MIN_DP:PL 0/0:32:84:31:0,84,1260 -20_10037292_10066351 3291 . G . . END=3291 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,1023 -20_10037292_10066351 3292 . G . . END=3293 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3294 . A . . END=3294 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,974 -20_10037292_10066351 3295 . A . . END=3297 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,986 -20_10037292_10066351 3298 . T . . END=3309 GT:DP:GQ:MIN_DP:PL 0/0:32:84:28:0,84,870 -20_10037292_10066351 3310 . A . . END=3310 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 3311 . A . . END=3313 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 3314 . A . . END=3314 GT:DP:GQ:MIN_DP:PL 0/0:30:77:30:0,77,873 -20_10037292_10066351 3315 . C . . END=3315 GT:DP:GQ:MIN_DP:PL 0/0:30:69:30:0,69,894 -20_10037292_10066351 3316 . T . . END=3316 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 3317 . G . . END=3317 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,864 -20_10037292_10066351 3318 . T . . END=3318 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3319 . C . . END=3319 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,945 -20_10037292_10066351 3320 . A . . END=3333 GT:DP:GQ:MIN_DP:PL 0/0:32:84:30:0,84,993 -20_10037292_10066351 3334 . A . . END=3334 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,979 -20_10037292_10066351 3335 . G . . END=3338 GT:DP:GQ:MIN_DP:PL 0/0:30:86:29:0,86,836 -20_10037292_10066351 3339 . C . . END=3341 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 3342 . C . . END=3342 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,870 -20_10037292_10066351 3343 . A . . END=3348 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,962 -20_10037292_10066351 3349 . A . . END=3349 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,1011 -20_10037292_10066351 3350 . G . . END=3351 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 3352 . A . . END=3352 GT:DP:GQ:MIN_DP:PL 0/0:36:87:36:0,87,1121 -20_10037292_10066351 3353 . G . . END=3361 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1163 -20_10037292_10066351 3362 . C . . END=3362 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1036 -20_10037292_10066351 3363 . A . . END=3364 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 3365 . A . . END=3365 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1067 -20_10037292_10066351 3366 . C . . END=3369 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1142 -20_10037292_10066351 3370 . C . . END=3370 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1138 -20_10037292_10066351 3371 . A . . END=3418 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,108,1248 -20_10037292_10066351 3419 . T . . END=3419 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1188 -20_10037292_10066351 3420 . T . . END=3436 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1140 -20_10037292_10066351 3437 . T . . END=3437 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1118 -20_10037292_10066351 3438 . T . . END=3439 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,103,1164 -20_10037292_10066351 3440 . A . . END=3440 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1216 -20_10037292_10066351 3441 . T . . END=3444 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,105,1575 -20_10037292_10066351 3445 . G . . END=3446 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1100 -20_10037292_10066351 3447 . C . . END=3453 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 3454 . G . . END=3458 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1043 -20_10037292_10066351 3459 . T . . END=3459 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1134 -20_10037292_10066351 3460 . T . . END=3460 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 3461 . C . . END=3468 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,101,1112 -20_10037292_10066351 3469 . C . . END=3469 GT:DP:GQ:MIN_DP:PL 0/0:39:60:39:0,60,1079 -20_10037292_10066351 3470 . T . . END=3474 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,99,1485 -20_10037292_10066351 3475 . C . . END=3475 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1064 -20_10037292_10066351 3476 . T . . END=3478 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,102,1530 -20_10037292_10066351 3479 . T . . END=3479 GT:DP:GQ:MIN_DP:PL 0/0:44:57:44:0,57,1177 -20_10037292_10066351 3480 . C CT, 742.03 . DP=30;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=108000,30 GT:AD:DP:GQ:PL:SB 1/1:0,26,0:26:78:756,78,0,756,78,756:0,0,15,11 -20_10037292_10066351 3481 . T . . END=3486 GT:DP:GQ:MIN_DP:PL 0/0:28:72:26:0,72,1080 -20_10037292_10066351 3487 . T . . END=3487 GT:DP:GQ:MIN_DP:PL 0/0:26:69:26:0,69,1035 -20_10037292_10066351 3488 . T . . END=3489 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 3490 . C . . END=3490 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,818 -20_10037292_10066351 3491 . A . . END=3491 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3492 . A . . END=3492 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 3493 . T . . END=3496 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3497 . C . . END=3497 GT:DP:GQ:MIN_DP:PL 0/0:29:71:29:0,71,802 -20_10037292_10066351 3498 . A . . END=3498 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 3499 . C . . END=3499 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 3500 . G . . END=3501 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 3502 . A . . END=3512 GT:DP:GQ:MIN_DP:PL 0/0:28:72:26:0,72,1080 -20_10037292_10066351 3513 . A . . END=3513 GT:DP:GQ:MIN_DP:PL 0/0:26:62:26:0,62,772 -20_10037292_10066351 3514 . T . . END=3519 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 3520 . AT A, 760.03 . DP=28;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=100800,28 GT:AD:DP:GQ:PL:SB 1/1:0,26,0:26:78:774,78,0,774,78,774:0,0,15,11 -20_10037292_10066351 3522 . T . . END=3523 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,114,1710 -20_10037292_10066351 3524 . T . . END=3524 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1092 -20_10037292_10066351 3525 . T . . END=3529 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1194 -20_10037292_10066351 3530 . A . . END=3531 GT:DP:GQ:MIN_DP:PL 0/0:39:92:38:0,92,1099 -20_10037292_10066351 3532 . A . . END=3532 GT:DP:GQ:MIN_DP:PL 0/0:38:65:38:0,65,1022 -20_10037292_10066351 3533 . A . . END=3535 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 3536 . G . . END=3536 GT:DP:GQ:MIN_DP:PL 0/0:39:67:39:0,67,996 -20_10037292_10066351 3537 . A . . END=3547 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,108,1620 -20_10037292_10066351 3548 . G . . END=3548 GT:DP:GQ:MIN_DP:PL 0/0:38:86:38:0,86,1042 -20_10037292_10066351 3549 . T . . END=3550 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1165 -20_10037292_10066351 3551 . A . . END=3551 GT:DP:GQ:MIN_DP:PL 0/0:38:94:38:0,94,1105 -20_10037292_10066351 3552 . A . . END=3552 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3553 . C . . END=3555 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1070 -20_10037292_10066351 3556 . C . . END=3562 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,100,1084 -20_10037292_10066351 3563 . C . . END=3563 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1080 -20_10037292_10066351 3564 . A . . END=3570 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,108,1206 -20_10037292_10066351 3571 . C . . END=3571 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1114 -20_10037292_10066351 3572 . A . . END=3576 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,102,1145 -20_10037292_10066351 3577 . G . . END=3577 GT:DP:GQ:MIN_DP:PL 0/0:41:83:41:0,83,1163 -20_10037292_10066351 3578 . A . . END=3579 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,112,1139 -20_10037292_10066351 3580 . T . . END=3580 GT:DP:GQ:MIN_DP:PL 0/0:43:94:43:0,94,1150 -20_10037292_10066351 3581 . T . . END=3593 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,100,1153 -20_10037292_10066351 3594 . C . . END=3595 GT:DP:GQ:MIN_DP:PL 0/0:40:94:39:0,94,1054 -20_10037292_10066351 3596 . T . . END=3596 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,109,1244 -20_10037292_10066351 3597 . C . . END=3597 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1101 -20_10037292_10066351 3598 . T . . END=3599 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,102,1530 -20_10037292_10066351 3600 . T . . END=3600 GT:DP:GQ:MIN_DP:PL 0/0:41:95:41:0,95,1208 -20_10037292_10066351 3601 . T . . END=3601 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,105,1575 -20_10037292_10066351 3602 . A . . END=3603 GT:DP:GQ:MIN_DP:PL 0/0:41:75:40:0,75,1125 -20_10037292_10066351 3604 . G . . END=3604 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,105,1575 -20_10037292_10066351 3605 . C . . END=3605 GT:DP:GQ:MIN_DP:PL 0/0:42:62:42:0,62,1050 -20_10037292_10066351 3606 . C . . END=3611 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,99,1485 -20_10037292_10066351 3612 . G . . END=3612 GT:DP:GQ:MIN_DP:PL 0/0:39:63:39:0,63,1081 -20_10037292_10066351 3613 . T . . END=3613 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,102,1530 -20_10037292_10066351 3614 . G . . END=3614 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1152 -20_10037292_10066351 3615 . C . . END=3615 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,105,1575 -20_10037292_10066351 3616 . A . . END=3616 GT:DP:GQ:MIN_DP:PL 0/0:40:69:40:0,69,1125 -20_10037292_10066351 3617 . T . . END=3622 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1485 -20_10037292_10066351 3623 . T . . END=3623 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1048 -20_10037292_10066351 3624 . A . . END=3625 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1152 -20_10037292_10066351 3626 . G . . END=3628 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,105,1121 -20_10037292_10066351 3629 . T . . END=3629 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1081 -20_10037292_10066351 3630 . C . . END=3630 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1015 -20_10037292_10066351 3631 . T . . END=3631 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 3632 . C . . END=3632 GT:DP:GQ:MIN_DP:PL 0/0:34:59:34:0,59,951 -20_10037292_10066351 3633 . T . . END=3633 GT:DP:GQ:MIN_DP:PL 0/0:35:91:35:0,91,1033 -20_10037292_10066351 3634 . C . . END=3634 GT:DP:GQ:MIN_DP:PL 0/0:35:68:35:0,68,974 -20_10037292_10066351 3635 . A . . END=3641 GT:DP:GQ:MIN_DP:PL 0/0:36:91:35:0,91,1085 -20_10037292_10066351 3642 . C . . END=3642 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,900 -20_10037292_10066351 3643 . G . . END=3651 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1171 -20_10037292_10066351 3652 . A . . END=3652 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1126 -20_10037292_10066351 3653 . G . . END=3667 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,99,1092 -20_10037292_10066351 3668 . A . . END=3668 GT:DP:GQ:MIN_DP:PL 0/0:44:76:44:0,76,1248 -20_10037292_10066351 3669 . T . . END=3672 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,120,1800 -20_10037292_10066351 3673 . T . . END=3673 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1192 -20_10037292_10066351 3674 . G . . END=3674 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,101,1251 -20_10037292_10066351 3675 . A . . END=3675 GT:DP:GQ:MIN_DP:PL 0/0:42:88:42:0,88,1126 -20_10037292_10066351 3676 . A . . END=3683 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,113,1311 -20_10037292_10066351 3684 . C . . END=3684 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1257 -20_10037292_10066351 3685 . T . . END=3685 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,120,1800 -20_10037292_10066351 3686 . C . . END=3686 GT:DP:GQ:MIN_DP:PL 0/0:43:93:43:0,93,1225 -20_10037292_10066351 3687 . C . . END=3693 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,113,1254 -20_10037292_10066351 3694 . A . . END=3694 GT:DP:GQ:MIN_DP:PL 0/0:44:80:44:0,80,1185 -20_10037292_10066351 3695 . G . . END=3769 GT:DP:GQ:MIN_DP:PL 0/0:47:99:41:0,100,1196 -20_10037292_10066351 3770 . A . . END=3770 GT:DP:GQ:MIN_DP:PL 0/0:48:88:48:0,88,1268 -20_10037292_10066351 3771 . A . . END=3780 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,106,1300 -20_10037292_10066351 3781 . C . . END=3781 GT:DP:GQ:MIN_DP:PL 0/0:44:85:44:0,85,1222 -20_10037292_10066351 3782 . T . . END=3784 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,120,1800 -20_10037292_10066351 3785 . G . . END=3785 GT:DP:GQ:MIN_DP:PL 0/0:44:97:44:0,97,1329 -20_10037292_10066351 3786 . T . . END=3834 GT:DP:GQ:MIN_DP:PL 0/0:44:99:36:0,105,1125 -20_10037292_10066351 3835 . T . . END=3835 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1163 -20_10037292_10066351 3836 . C . . END=3836 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 3837 . C . . END=3837 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1117 -20_10037292_10066351 3838 . T . . END=3857 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,102,1041 -20_10037292_10066351 3858 . G . . END=3867 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 3868 . T . . END=3868 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,911 -20_10037292_10066351 3869 . G . . END=3870 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 3871 . A . . END=3871 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,927 -20_10037292_10066351 3872 . C . . END=3872 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 3873 . T . . END=3873 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,914 -20_10037292_10066351 3874 . G . . END=3877 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 3878 . A . . END=3883 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 3884 . T . . END=3884 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 3885 . T . . END=3885 GT:DP:GQ:MIN_DP:PL 0/0:35:79:35:0,79,1031 -20_10037292_10066351 3886 . C . . END=3890 GT:DP:GQ:MIN_DP:PL 0/0:35:81:34:0,81,1215 -20_10037292_10066351 3891 . G . . END=3893 GT:DP:GQ:MIN_DP:PL 0/0:38:90:35:0,90,1137 -20_10037292_10066351 3894 . C . . END=3899 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,1485 -20_10037292_10066351 3900 . C . . END=3900 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1069 -20_10037292_10066351 3901 . A . . END=3901 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 3902 . A . . END=3902 GT:DP:GQ:MIN_DP:PL 0/0:38:54:38:0,54,1082 -20_10037292_10066351 3903 . G . . END=3906 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1530 -20_10037292_10066351 3907 . G . . END=3907 GT:DP:GQ:MIN_DP:PL 0/0:37:88:37:0,88,1135 -20_10037292_10066351 3908 . C . . END=3929 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1183 -20_10037292_10066351 3930 . T . . END=3936 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 3937 . A . . END=3942 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 3943 . T . . END=3948 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,960 -20_10037292_10066351 3949 . A . . END=3949 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,932 -20_10037292_10066351 3950 . G . . END=3955 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,959 -20_10037292_10066351 3956 . A . . END=3956 GT:DP:GQ:MIN_DP:PL 0/0:31:70:31:0,70,941 -20_10037292_10066351 3957 . C . . END=3965 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,920 -20_10037292_10066351 3966 . T . . END=3966 GT:DP:GQ:MIN_DP:PL 0/0:33:86:33:0,86,1005 -20_10037292_10066351 3967 . A . . END=3967 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 3968 . G . . END=3968 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,1014 -20_10037292_10066351 3969 . C . . END=3975 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 3976 . A . . END=3980 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 -20_10037292_10066351 3981 . A . . END=3983 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,917 -20_10037292_10066351 3984 . A . . END=3987 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 3988 . G . . END=3997 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,914 -20_10037292_10066351 3998 . T . . END=4000 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 4001 . A . . END=4001 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1030 -20_10037292_10066351 4002 . A . . END=4006 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1047 -20_10037292_10066351 4007 . C . . END=4007 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,1026 -20_10037292_10066351 4008 . A . . END=4010 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 4011 . T . . END=4011 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 4012 . C T, 1092.06 . DP=36;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=129600,36 GT:AD:DP:GQ:PL:SB 1/1:0,35,0:35:99:1106,105,0,1106,105,1106:0,0,19,16 -20_10037292_10066351 4013 . G . . END=4013 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1305 -20_10037292_10066351 4014 . G . . END=4017 GT:DP:GQ:MIN_DP:PL 0/0:37:90:35:0,90,1350 -20_10037292_10066351 4018 . A . . END=4019 GT:DP:GQ:MIN_DP:PL 0/0:35:78:35:0,78,1170 -20_10037292_10066351 4020 . T . . END=4024 GT:DP:GQ:MIN_DP:PL 0/0:36:81:35:0,81,1215 -20_10037292_10066351 4025 . A . . END=4031 GT:DP:GQ:MIN_DP:PL 0/0:33:72:28:0,72,1080 -20_10037292_10066351 4032 . T . . END=4034 GT:DP:GQ:MIN_DP:PL 0/0:30:66:28:0,66,990 -20_10037292_10066351 4035 . G T, 0 . BaseQRankSum=-2.303;DP=30;ExcessHet=0.0000;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=108000,30;ReadPosRankSum=1.760 GT:AD:DP:GQ:PL:SB 0/0:25,2,0:27:60:0,60,734,74,739,753:14,11,1,1 -20_10037292_10066351 4036 . T . . END=4040 GT:DP:GQ:MIN_DP:PL 0/0:27:63:26:0,63,945 -20_10037292_10066351 4041 . T . . END=4043 GT:DP:GQ:MIN_DP:PL 0/0:29:75:27:0,75,1125 -20_10037292_10066351 4044 . T . . END=4050 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 4051 . C . . END=4053 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 4054 . G . . END=4061 GT:DP:GQ:MIN_DP:PL 0/0:31:81:28:0,81,1215 -20_10037292_10066351 4062 . A . . END=4066 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4067 . C . . END=4067 GT:DP:GQ:MIN_DP:PL 0/0:32:73:32:0,73,937 -20_10037292_10066351 4068 . A . . END=4081 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,101,1033 -20_10037292_10066351 4082 . C . . END=4082 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1154 -20_10037292_10066351 4083 . T . . END=4106 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1167 -20_10037292_10066351 4107 . G . . END=4107 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1286 -20_10037292_10066351 4108 . G . . END=4139 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1071 -20_10037292_10066351 4140 . T . . END=4141 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1135 -20_10037292_10066351 4142 . A . . END=4177 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,100,1167 -20_10037292_10066351 4178 . A . . END=4186 GT:DP:GQ:MIN_DP:PL 0/0:38:90:36:0,90,1350 -20_10037292_10066351 4187 . T . . END=4191 GT:DP:GQ:MIN_DP:PL 0/0:37:87:33:0,87,1305 -20_10037292_10066351 4192 . G . . END=4192 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4193 . A . . END=4193 GT:DP:GQ:MIN_DP:PL 0/0:35:94:35:0,94,1028 -20_10037292_10066351 4194 . C . . END=4194 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4195 . T . . END=4196 GT:DP:GQ:MIN_DP:PL 0/0:35:85:35:0,85,1066 -20_10037292_10066351 4197 . T . . END=4200 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1040 -20_10037292_10066351 4201 . G . . END=4201 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1117 -20_10037292_10066351 4202 . G . . END=4208 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 4209 . G . . END=4210 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1395 -20_10037292_10066351 4211 . C . . END=4212 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 4213 . T . . END=4214 GT:DP:GQ:MIN_DP:PL 0/0:38:93:37:0,93,1395 -20_10037292_10066351 4215 . A . . END=4219 GT:DP:GQ:MIN_DP:PL 0/0:37:80:34:0,80,1158 -20_10037292_10066351 4220 . T . . END=4225 GT:DP:GQ:MIN_DP:PL 0/0:36:93:34:0,93,1395 -20_10037292_10066351 4226 . G . . END=4226 GT:DP:GQ:MIN_DP:PL 0/0:34:67:34:0,67,1017 -20_10037292_10066351 4227 . T . . END=4232 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 4233 . C . . END=4233 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1039 -20_10037292_10066351 4234 . C . . END=4235 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,101,1014 -20_10037292_10066351 4236 . A . . END=4236 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,1043 -20_10037292_10066351 4237 . T . . END=4376 GT:DP:GQ:MIN_DP:PL 0/0:46:99:36:0,105,1190 -20_10037292_10066351 4377 . T . . END=4377 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1282 -20_10037292_10066351 4378 . C . . END=4389 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,102,1234 -20_10037292_10066351 4390 . A . . END=4390 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1120 -20_10037292_10066351 4391 . T . . END=4391 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1119 -20_10037292_10066351 4392 . C . . END=4393 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4394 . A . . END=4398 GT:DP:GQ:MIN_DP:PL 0/0:36:90:35:0,90,1350 -20_10037292_10066351 4399 . A . . END=4399 GT:DP:GQ:MIN_DP:PL 0/0:36:88:36:0,88,1098 -20_10037292_10066351 4400 . T . . END=4403 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1070 -20_10037292_10066351 4404 . A . . END=4404 GT:DP:GQ:MIN_DP:PL 0/0:35:28:35:0,28,953 -20_10037292_10066351 4405 . A . . END=4405 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 4406 . C . . END=4407 GT:DP:GQ:MIN_DP:PL 0/0:28:66:28:0,66,990 -20_10037292_10066351 4408 . T . . END=4408 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 4409 . A ATG,ATATG, 785.03 . DP=31;ExcessHet=0.0000;MLEAC=0,2,0;MLEAF=0.00,1.00,0.00;RAW_MQandDP=111600,31 GT:AD:DP:GQ:PL:SB 2/2:0,0,24,0:24:72:799,867,1161,72,87,0,850,1031,87,980:0,0,13,11 -20_10037292_10066351 4410 . T . . END=4410 GT:DP:GQ:MIN_DP:PL 0/0:35:81:35:0,81,1215 -20_10037292_10066351 4411 . G . . END=4411 GT:DP:GQ:MIN_DP:PL 0/0:34:0:34:0,0,738 -20_10037292_10066351 4412 . T . . END=4412 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 4413 . G . . END=4416 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 -20_10037292_10066351 4417 . G . . END=4422 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 4423 . G . . END=4423 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1108 -20_10037292_10066351 4424 . T . . END=4426 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 4427 . G . . END=4427 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1091 -20_10037292_10066351 4428 . T . . END=4430 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1137 -20_10037292_10066351 4431 . G . . END=4435 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 4436 . C . . END=4436 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1161 -20_10037292_10066351 4437 . A . . END=4473 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,108,1286 -20_10037292_10066351 4474 . A . . END=4474 GT:DP:GQ:MIN_DP:PL 0/0:45:87:45:0,87,1273 -20_10037292_10066351 4475 . G . . END=4479 GT:DP:GQ:MIN_DP:PL 0/0:46:99:44:0,103,1305 -20_10037292_10066351 4480 . G . . END=4480 GT:DP:GQ:MIN_DP:PL 0/0:46:89:46:0,89,1235 -20_10037292_10066351 4481 . G . . END=4502 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,106,1289 -20_10037292_10066351 4503 . G . . END=4503 GT:DP:GQ:MIN_DP:PL 0/0:43:67:43:0,67,1218 -20_10037292_10066351 4504 . A . . END=4592 GT:DP:GQ:MIN_DP:PL 0/0:50:99:42:0,99,1431 -20_10037292_10066351 4593 . G . . END=4593 GT:DP:GQ:MIN_DP:PL 0/0:40:96:40:0,96,1440 -20_10037292_10066351 4594 . T . . END=4604 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 -20_10037292_10066351 4605 . T . . END=4608 GT:DP:GQ:MIN_DP:PL 0/0:36:96:35:0,96,1440 -20_10037292_10066351 4609 . C . . END=4610 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 4611 . G . . END=4611 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 4612 . G . . END=4615 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 4616 . G . . END=4616 GT:DP:GQ:MIN_DP:PL 0/0:34:86:34:0,86,932 -20_10037292_10066351 4617 . T . . END=4622 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 4623 . A . . END=4623 GT:DP:GQ:MIN_DP:PL 0/0:37:85:37:0,85,983 -20_10037292_10066351 4624 . C . . END=4630 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1094 -20_10037292_10066351 4631 . C . . END=4631 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1118 -20_10037292_10066351 4632 . C . . END=4639 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,101,1156 -20_10037292_10066351 4640 . A . . END=4640 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1108 -20_10037292_10066351 4641 . T . . END=4649 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1217 -20_10037292_10066351 4650 . T . . END=4655 GT:DP:GQ:MIN_DP:PL 0/0:38:93:36:0,93,1395 -20_10037292_10066351 4656 . C . . END=4666 GT:DP:GQ:MIN_DP:PL 0/0:33:84:30:0,84,1260 -20_10037292_10066351 4667 . C . . END=4674 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 4675 . A . . END=4682 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1021 -20_10037292_10066351 4683 . G . . END=4683 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1011 -20_10037292_10066351 4684 . A . . END=4684 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1173 -20_10037292_10066351 4685 . G . . END=4685 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1121 -20_10037292_10066351 4686 . C . . END=4690 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,107,1013 -20_10037292_10066351 4691 . G . . END=4691 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,997 -20_10037292_10066351 4692 . C . . END=4704 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,101,1183 -20_10037292_10066351 4705 . A . . END=4706 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1107 -20_10037292_10066351 4707 . A . . END=4718 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,102,1185 -20_10037292_10066351 4719 . T . . END=4719 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1078 -20_10037292_10066351 4720 . A . . END=4724 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 4725 . C . . END=4725 GT:DP:GQ:MIN_DP:PL 0/0:40:81:40:0,81,1101 -20_10037292_10066351 4726 . A . . END=4733 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,101,1155 -20_10037292_10066351 4734 . C . . END=4734 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1188 -20_10037292_10066351 4735 . T . . END=4735 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,103,1187 -20_10037292_10066351 4736 . A . . END=4736 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1108 -20_10037292_10066351 4737 . C . . END=4739 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,99,1188 -20_10037292_10066351 4740 . T . . END=4740 GT:DP:GQ:MIN_DP:PL 0/0:41:94:41:0,94,1197 -20_10037292_10066351 4741 . A . . END=4746 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,105,1575 -20_10037292_10066351 4747 . T . . END=4747 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1082 -20_10037292_10066351 4748 . T . . END=4748 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 4749 . T . . END=4750 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1092 -20_10037292_10066351 4751 . T . . END=4752 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1170 -20_10037292_10066351 4753 . A . . END=4753 GT:DP:GQ:MIN_DP:PL 0/0:35:64:35:0,64,1027 -20_10037292_10066351 4754 . T . . END=4754 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 4755 . A . . END=4755 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1112 -20_10037292_10066351 4756 . A . . END=4757 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1575 -20_10037292_10066351 4758 . C . . END=4758 GT:DP:GQ:MIN_DP:PL 0/0:40:73:40:0,73,1197 -20_10037292_10066351 4759 . A . . END=4790 GT:DP:GQ:MIN_DP:PL 0/0:43:99:36:0,102,1163 -20_10037292_10066351 4791 . G . . END=4791 GT:DP:GQ:MIN_DP:PL 0/0:45:83:45:0,83,1299 -20_10037292_10066351 4792 . A . . END=4889 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,100,1187 -20_10037292_10066351 4890 . C . . END=4890 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1215 -20_10037292_10066351 4891 . T . . END=4895 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 4896 . A . . END=4898 GT:DP:GQ:MIN_DP:PL 0/0:39:96:37:0,96,1440 -20_10037292_10066351 4899 . A . . END=4904 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 4905 . A . . END=4912 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,1060 -20_10037292_10066351 4913 . T . . END=4926 GT:DP:GQ:MIN_DP:PL 0/0:33:84:29:0,84,1260 -20_10037292_10066351 4927 . C . . END=4927 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,819 -20_10037292_10066351 4928 . A . . END=4931 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 4932 . G . . END=4932 GT:DP:GQ:MIN_DP:PL 0/0:30:67:30:0,67,865 -20_10037292_10066351 4933 . A . . END=4933 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,910 -20_10037292_10066351 4934 . C . . END=4946 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 4947 . A . . END=4949 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 4950 . A . . END=4950 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 4951 . T . . END=4957 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 4958 . G . . END=4958 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 4959 . A . . END=4967 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1096 -20_10037292_10066351 4968 . A . . END=5026 GT:DP:GQ:MIN_DP:PL 0/0:43:99:36:0,102,1168 -20_10037292_10066351 5027 . C T, 1377.06 . DP=44;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=158400,44 GT:AD:DP:GQ:PL:SB 1/1:0,44,0:44:99:1391,132,0,1391,132,1391:0,0,22,22 -20_10037292_10066351 5028 . C . . END=5204 GT:DP:GQ:MIN_DP:PL 0/0:48:99:38:0,99,1306 -20_10037292_10066351 5205 . A . . END=5205 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1100 -20_10037292_10066351 5206 . A . . END=5211 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,111,1107 -20_10037292_10066351 5212 . A . . END=5212 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1096 -20_10037292_10066351 5213 . T . . END=5226 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1240 -20_10037292_10066351 5227 . G . . END=5227 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1272 -20_10037292_10066351 5228 . G . . END=5362 GT:DP:GQ:MIN_DP:PL 0/0:49:99:38:0,102,1184 -20_10037292_10066351 5363 . T . . END=5363 GT:DP:GQ:MIN_DP:PL 0/0:49:97:49:0,97,1426 -20_10037292_10066351 5364 . G . . END=5373 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,120,1800 -20_10037292_10066351 5374 . T . . END=5374 GT:DP:GQ:MIN_DP:PL 0/0:46:83:46:0,83,1368 -20_10037292_10066351 5375 . G . . END=5388 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,108,1301 -20_10037292_10066351 5389 . T . . END=5389 GT:DP:GQ:MIN_DP:PL 0/0:43:96:43:0,96,1317 -20_10037292_10066351 5390 . G . . END=5417 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,99,1206 -20_10037292_10066351 5418 . A . . END=5422 GT:DP:GQ:MIN_DP:PL 0/0:40:90:39:0,90,1112 -20_10037292_10066351 5423 . C . . END=5430 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,99,1485 -20_10037292_10066351 5431 . T . . END=5431 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1161 -20_10037292_10066351 5432 . T . . END=5439 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1121 -20_10037292_10066351 5440 . T . . END=5440 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 5441 . G . . END=5441 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 5442 . C . . END=5449 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1171 -20_10037292_10066351 5450 . T . . END=5452 GT:DP:GQ:MIN_DP:PL 0/0:35:87:34:0,87,1305 -20_10037292_10066351 5453 . A . . END=5453 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,1064 -20_10037292_10066351 5454 . G . . END=5454 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1350 -20_10037292_10066351 5455 . A . . END=5455 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,968 -20_10037292_10066351 5456 . A . . END=5458 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 5459 . A . . END=5459 GT:DP:GQ:MIN_DP:PL 0/0:34:81:34:0,81,1051 -20_10037292_10066351 5460 . A . . END=5460 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,1029 -20_10037292_10066351 5461 . G . . END=5461 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 5462 . A . . END=5462 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,995 -20_10037292_10066351 5463 . T . . END=5464 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5465 . A . . END=5465 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,1030 -20_10037292_10066351 5466 . A . . END=5466 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1025 -20_10037292_10066351 5467 . T . . END=5467 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5468 . G . . END=5468 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5469 . A G, 862.06 . DP=29;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=104400,29 GT:AD:DP:GQ:PL:SB 1/1:0,29,0:29:86:876,86,0,876,86,876:0,0,14,15 -20_10037292_10066351 5470 . G . . END=5470 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,999 -20_10037292_10066351 5471 . C . . END=5471 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5472 . A . . END=5472 GT:DP:GQ:MIN_DP:PL 0/0:34:80:34:0,80,1066 -20_10037292_10066351 5473 . A . . END=5473 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 5474 . G . . END=5477 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 5478 . A . . END=5478 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,1012 -20_10037292_10066351 5479 . G . . END=5479 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 5480 . C . . END=5483 GT:DP:GQ:MIN_DP:PL 0/0:34:96:33:0,96,1440 -20_10037292_10066351 5484 . G . . END=5484 GT:DP:GQ:MIN_DP:PL 0/0:33:65:33:0,65,1006 -20_10037292_10066351 5485 . A . . END=5492 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 5493 . T . . END=5493 GT:DP:GQ:MIN_DP:PL 0/0:33:62:33:0,62,918 -20_10037292_10066351 5494 . T . . END=5494 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1017 -20_10037292_10066351 5495 . T . . END=5495 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1098 -20_10037292_10066351 7536 . C . . END=7536 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,103,1287 -20_10037292_10066351 7537 . C . . END=7537 GT:DP:GQ:MIN_DP:PL 0/0:43:85:43:0,85,1165 -20_10037292_10066351 7538 . C . . END=7552 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,102,1206 -20_10037292_10066351 7553 . A . . END=7553 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1289 -20_10037292_10066351 7554 . A . . END=7555 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1162 -20_10037292_10066351 7556 . C . . END=7556 GT:DP:GQ:MIN_DP:PL 0/0:38:69:38:0,69,1008 -20_10037292_10066351 7557 . A G, 996.06 . DP=38;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=136800,38 GT:AD:DP:GQ:PL:SB 1/1:0,37,0:37:99:1010,108,0,1010,108,1010:0,0,16,21 -20_10037292_10066351 7558 . C . . END=7559 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 7560 . C . . END=7560 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1020 -20_10037292_10066351 7561 . G . . END=7561 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 7562 . G . . END=7562 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1124 -20_10037292_10066351 7563 . T . . END=7566 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1575 -20_10037292_10066351 7567 . G . . END=7567 GT:DP:GQ:MIN_DP:PL 0/0:39:88:39:0,88,1137 -20_10037292_10066351 7568 . G . . END=7569 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,99,1485 -20_10037292_10066351 7570 . C . . END=7574 GT:DP:GQ:MIN_DP:PL 0/0:37:96:35:0,96,1440 -20_10037292_10066351 7575 . T . . END=7581 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,1215 -20_10037292_10066351 7582 . T . . END=7584 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1170 -20_10037292_10066351 7585 . G . . END=7591 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 7592 . T . . END=7602 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,772 -20_10037292_10066351 7603 . T . . END=7609 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 7610 . G . . END=7610 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 7611 . A . . END=7611 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,994 -20_10037292_10066351 7612 . G . . END=7630 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,991 -20_10037292_10066351 7631 . T . . END=7635 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1054 -20_10037292_10066351 7636 . G . . END=7639 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 7640 . T . . END=7653 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,99,1241 -20_10037292_10066351 7654 . G . . END=7654 GT:DP:GQ:MIN_DP:PL 0/0:41:82:41:0,82,1213 -20_10037292_10066351 7655 . C . . END=7658 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,115,1317 -20_10037292_10066351 7659 . G . . END=7659 GT:DP:GQ:MIN_DP:PL 0/0:43:90:43:0,90,1260 -20_10037292_10066351 7660 . T . . END=7675 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,101,1234 -20_10037292_10066351 7676 . G . . END=7676 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1157 -20_10037292_10066351 7677 . T . . END=7680 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,108,1219 -20_10037292_10066351 7681 . C . . END=7681 GT:DP:GQ:MIN_DP:PL 0/0:40:62:40:0,62,1083 -20_10037292_10066351 7682 . C . . END=7684 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,106,1189 -20_10037292_10066351 7685 . G . . END=7685 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1207 -20_10037292_10066351 7686 . T . . END=7694 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,100,1179 -20_10037292_10066351 7695 . G . . END=7695 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1216 -20_10037292_10066351 7696 . T . . END=7696 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,115,1278 -20_10037292_10066351 7697 . A . . END=7697 GT:DP:GQ:MIN_DP:PL 0/0:42:85:42:0,85,1238 -20_10037292_10066351 7698 . C . . END=7724 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,99,1244 -20_10037292_10066351 7725 . C . . END=7725 GT:DP:GQ:MIN_DP:PL 0/0:44:91:44:0,91,1217 -20_10037292_10066351 7726 . A . . END=7785 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,100,1272 -20_10037292_10066351 7786 . G T, 1380.06 . DP=44;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=158400,44 GT:AD:DP:GQ:PL:SB 1/1:0,44,0:44:99:1394,132,0,1394,132,1394:0,0,22,22 -20_10037292_10066351 7787 . C . . END=7822 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,105,1208 -20_10037292_10066351 7823 . A . . END=7823 GT:DP:GQ:MIN_DP:PL 0/0:45:96:45:0,96,1299 -20_10037292_10066351 7824 . C . . END=7824 GT:DP:GQ:MIN_DP:PL 0/0:45:99:45:0,112,1315 -20_10037292_10066351 7825 . C . . END=7825 GT:DP:GQ:MIN_DP:PL 0/0:44:84:44:0,84,1272 -20_10037292_10066351 7826 . T . . END=7860 GT:DP:GQ:MIN_DP:PL 0/0:42:99:35:0,105,1100 -20_10037292_10066351 7861 . A . . END=7861 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1124 -20_10037292_10066351 7862 . G . . END=7863 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,110,1094 -20_10037292_10066351 7864 . G . . END=7864 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1019 -20_10037292_10066351 7865 . C . . END=7871 GT:DP:GQ:MIN_DP:PL 0/0:39:99:35:0,105,1050 -20_10037292_10066351 7872 . A . . END=7872 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1192 -20_10037292_10066351 7873 . G . . END=7891 GT:DP:GQ:MIN_DP:PL 0/0:42:99:39:0,99,1187 -20_10037292_10066351 7892 . C . . END=7892 GT:DP:GQ:MIN_DP:PL 0/0:40:89:40:0,89,1259 -20_10037292_10066351 7893 . T . . END=7894 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 7895 . C . . END=7895 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1213 -20_10037292_10066351 7896 . C . . END=7899 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,102,1530 -20_10037292_10066351 7900 . T . . END=7904 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1160 -20_10037292_10066351 7905 . C . . END=7908 GT:DP:GQ:MIN_DP:PL 0/0:35:87:34:0,87,1029 -20_10037292_10066351 7909 . T . . END=7909 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 7910 . G . . END=7911 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 -20_10037292_10066351 7912 . A . . END=7912 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,988 -20_10037292_10066351 7913 . C . . END=7931 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,864 -20_10037292_10066351 7932 . A . . END=7932 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,934 -20_10037292_10066351 7933 . T . . END=7933 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,906 -20_10037292_10066351 7934 . A . . END=7934 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,896 -20_10037292_10066351 7935 . G . . END=7935 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,992 -20_10037292_10066351 7936 . G . . END=7936 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,924 -20_10037292_10066351 7937 . G . . END=7937 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,976 -20_10037292_10066351 7938 . G . . END=7939 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 7940 . A . . END=7949 GT:DP:GQ:MIN_DP:PL 0/0:30:72:29:0,72,974 -20_10037292_10066351 7950 . A . . END=7950 GT:DP:GQ:MIN_DP:PL 0/0:31:57:31:0,57,888 -20_10037292_10066351 7951 . A . . END=7956 GT:DP:GQ:MIN_DP:PL 0/0:29:75:27:0,75,1125 -20_10037292_10066351 7957 . T . . END=7957 GT:DP:GQ:MIN_DP:PL 0/0:26:50:26:0,50,787 -20_10037292_10066351 7958 . G . . END=7958 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 7959 . G . . END=7959 GT:DP:GQ:MIN_DP:PL 0/0:25:42:25:0,42,696 -20_10037292_10066351 7960 . T . . END=7960 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 7961 . A . . END=7961 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,824 -20_10037292_10066351 7962 . T . . END=7964 GT:DP:GQ:MIN_DP:PL 0/0:27:72:25:0,72,772 -20_10037292_10066351 7965 . T . . END=7965 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,803 -20_10037292_10066351 7966 . A . . END=7967 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 7968 . C . . END=7998 GT:DP:GQ:MIN_DP:PL 0/0:24:60:22:0,60,900 -20_10037292_10066351 7999 . T . . END=7999 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,730 -20_10037292_10066351 8000 . T . . END=8002 GT:DP:GQ:MIN_DP:PL 0/0:25:67:25:0,67,801 -20_10037292_10066351 8003 . C . . END=8005 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 8006 . A . . END=8037 GT:DP:GQ:MIN_DP:PL 0/0:26:63:23:0,63,713 -20_10037292_10066351 8038 . G . . END=8038 GT:DP:GQ:MIN_DP:PL 0/0:23:57:23:0,57,723 -20_10037292_10066351 8039 . C . . END=8039 GT:DP:GQ:MIN_DP:PL 0/0:22:63:22:0,63,945 -20_10037292_10066351 8040 . A . . END=8040 GT:DP:GQ:MIN_DP:PL 0/0:22:44:22:0,44,674 -20_10037292_10066351 8041 . T . . END=8044 GT:DP:GQ:MIN_DP:PL 0/0:22:63:22:0,63,675 -20_10037292_10066351 8045 . G . . END=8045 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,771 -20_10037292_10066351 8046 . C . . END=8050 GT:DP:GQ:MIN_DP:PL 0/0:25:66:23:0,66,799 -20_10037292_10066351 8051 . C . . END=8061 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,1080 -20_10037292_10066351 8062 . C . . END=8063 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 -20_10037292_10066351 8064 . G . . END=8064 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8065 . C . . END=8065 GT:DP:GQ:MIN_DP:PL 0/0:25:61:25:0,61,727 -20_10037292_10066351 8066 . A . . END=8066 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8067 . A . . END=8067 GT:DP:GQ:MIN_DP:PL 0/0:25:58:25:0,58,727 -20_10037292_10066351 8068 . G . . END=8068 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8069 . T . . END=8069 GT:DP:GQ:MIN_DP:PL 0/0:26:64:26:0,64,763 -20_10037292_10066351 8070 . G . . END=8075 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8076 . A . . END=8076 GT:DP:GQ:MIN_DP:PL 0/0:25:63:25:0,63,723 -20_10037292_10066351 8077 . A . . END=8078 GT:DP:GQ:MIN_DP:PL 0/0:25:72:25:0,72,1080 -20_10037292_10066351 8079 . G . . END=8079 GT:DP:GQ:MIN_DP:PL 0/0:23:69:23:0,69,704 -20_10037292_10066351 8080 . C . . END=8086 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,671 -20_10037292_10066351 8087 . A . . END=8087 GT:DP:GQ:MIN_DP:PL 0/0:26:67:26:0,67,782 -20_10037292_10066351 8088 . C . . END=8088 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 8089 . A . . END=8089 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,783 -20_10037292_10066351 8090 . A . . END=8090 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8091 . G . . END=8091 GT:DP:GQ:MIN_DP:PL 0/0:29:62:29:0,62,814 -20_10037292_10066351 8092 . A . . END=8095 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,785 -20_10037292_10066351 8096 . A . . END=8102 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,899 -20_10037292_10066351 8103 . A . . END=8104 GT:DP:GQ:MIN_DP:PL 0/0:31:63:30:0,63,870 -20_10037292_10066351 8105 . A . . END=8106 GT:DP:GQ:MIN_DP:PL 0/0:31:74:30:0,74,895 -20_10037292_10066351 8107 . G . . END=8113 GT:DP:GQ:MIN_DP:PL 0/0:31:87:29:0,87,890 -20_10037292_10066351 8114 . G . . END=8114 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,967 -20_10037292_10066351 8115 . A . . END=8115 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 8116 . A . . END=8117 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,851 -20_10037292_10066351 8118 . A . . END=8119 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 8120 . A . . END=8124 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 8125 . A . . END=8125 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,969 -20_10037292_10066351 8126 . A . . END=8129 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,985 -20_10037292_10066351 8130 . C . . END=8131 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8132 . C . . END=8134 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8135 . C . . END=8142 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,1215 -20_10037292_10066351 8143 . G . . END=8151 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 -20_10037292_10066351 8152 . G . . END=8154 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1079 -20_10037292_10066351 8155 . A . . END=8155 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1065 -20_10037292_10066351 8156 . A . . END=8160 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,105,1122 -20_10037292_10066351 8161 . A . . END=8161 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1108 -20_10037292_10066351 8162 . T . . END=8179 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,101,1124 -20_10037292_10066351 8180 . G . . END=8180 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1035 -20_10037292_10066351 8181 . A . . END=8181 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1088 -20_10037292_10066351 8182 . T . . END=8182 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,995 -20_10037292_10066351 8183 . T . . END=8183 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1016 -20_10037292_10066351 8184 . T . . END=8206 GT:DP:GQ:MIN_DP:PL 0/0:40:99:33:0,99,1046 -20_10037292_10066351 8207 . C . . END=8207 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1199 -20_10037292_10066351 8208 . C . . END=8247 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,111,1280 -20_10037292_10066351 8248 . T . . END=8248 GT:DP:GQ:MIN_DP:PL 0/0:40:91:40:0,91,1108 -20_10037292_10066351 8249 . T . . END=8325 GT:DP:GQ:MIN_DP:PL 0/0:44:99:39:0,99,1177 -20_10037292_10066351 8326 . G . . END=8326 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1231 -20_10037292_10066351 8327 . A . . END=8333 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,105,1575 -20_10037292_10066351 8334 . A . . END=8334 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1440 -20_10037292_10066351 8335 . A . . END=8336 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,99,1485 -20_10037292_10066351 8337 . A . . END=8339 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1395 -20_10037292_10066351 8340 . T . . END=8349 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,99,1485 -20_10037292_10066351 8350 . G C, 1132.06 . DP=36;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=129600,36 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:1146,108,0,1146,108,1146:0,0,16,20 -20_10037292_10066351 8351 . A . . END=8354 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1160 -20_10037292_10066351 8355 . C . . END=8355 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1106 -20_10037292_10066351 8356 . T . . END=8391 GT:DP:GQ:MIN_DP:PL 0/0:37:99:33:0,99,1042 -20_10037292_10066351 8392 . T . . END=8392 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1069 -20_10037292_10066351 8393 . G . . END=8393 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 8394 . G . . END=8394 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 8395 . A . . END=8395 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1105 -20_10037292_10066351 8396 . G . . END=8396 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8397 . G . . END=8397 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1084 -20_10037292_10066351 8398 . C . . END=8398 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 8399 . A . . END=8407 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1350 -20_10037292_10066351 8408 . T . . END=8408 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,1047 -20_10037292_10066351 8409 . C . . END=8409 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8410 . C . . END=8410 GT:DP:GQ:MIN_DP:PL 0/0:34:51:34:0,51,981 -20_10037292_10066351 8411 . C . . END=8411 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1305 -20_10037292_10066351 8412 . T . . END=8422 GT:DP:GQ:MIN_DP:PL 0/0:30:75:28:0,75,1125 -20_10037292_10066351 8423 . T . . END=8425 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 8426 . C . . END=8433 GT:DP:GQ:MIN_DP:PL 0/0:29:74:28:0,74,918 -20_10037292_10066351 8434 . T . . END=8434 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8435 . G . . END=8439 GT:DP:GQ:MIN_DP:PL 0/0:30:72:28:0,72,1080 -20_10037292_10066351 8440 . C . . END=8440 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,857 -20_10037292_10066351 8441 . T . . END=8449 GT:DP:GQ:MIN_DP:PL 0/0:28:70:27:0,70,761 -20_10037292_10066351 8450 . C . . END=8450 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,821 -20_10037292_10066351 8451 . A . . END=8453 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 8454 . G . . END=8454 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,750 -20_10037292_10066351 8455 . T . . END=8456 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8457 . T . . END=8458 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,872 -20_10037292_10066351 8459 . G . . END=8460 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,912 -20_10037292_10066351 8461 . T . . END=8461 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,904 -20_10037292_10066351 8462 . C . . END=8462 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,846 -20_10037292_10066351 8463 . C . . END=8471 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,898 -20_10037292_10066351 8472 . C . . END=8472 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8473 . T . . END=8473 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,911 -20_10037292_10066351 8474 . C . . END=8479 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,900 -20_10037292_10066351 8480 . G . . END=8480 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8481 . G . . END=8483 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8484 . T . . END=8484 GT:DP:GQ:MIN_DP:PL 0/0:31:68:31:0,68,872 -20_10037292_10066351 8485 . T . . END=8490 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 8491 . G . . END=8491 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,744 -20_10037292_10066351 8492 . T . . END=8493 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 8494 . T . . END=8494 GT:DP:GQ:MIN_DP:PL 0/0:28:54:28:0,54,774 -20_10037292_10066351 8495 . G . . END=8496 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 8497 . G . . END=8497 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,759 -20_10037292_10066351 8498 . C . . END=8498 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,781 -20_10037292_10066351 8499 . T . . END=8502 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,780 -20_10037292_10066351 8503 . A . . END=8503 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,780 -20_10037292_10066351 8504 . C . . END=8514 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,1215 -20_10037292_10066351 8515 . A . . END=8520 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 8521 . C . . END=8525 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 8526 . A . . END=8526 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1049 -20_10037292_10066351 8527 . T . . END=8586 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,99,1078 -20_10037292_10066351 8587 . C . . END=8587 GT:DP:GQ:MIN_DP:PL 0/0:39:68:39:0,68,1117 -20_10037292_10066351 8588 . C . . END=8589 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 8590 . G . . END=8590 GT:DP:GQ:MIN_DP:PL 0/0:39:85:39:0,85,1204 -20_10037292_10066351 8591 . C . . END=8591 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 8592 . T . . END=8592 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1174 -20_10037292_10066351 8593 . G . . END=8594 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,105,1085 -20_10037292_10066351 8595 . T . . END=8595 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,1078 -20_10037292_10066351 8596 . C . . END=8596 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8597 . C . . END=8599 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 8600 . T . . END=8600 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 8601 . G . . END=8601 GT:DP:GQ:MIN_DP:PL 0/0:36:82:36:0,82,1089 -20_10037292_10066351 8602 . A . . END=8604 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 8605 . A . . END=8615 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 8616 . A . . END=8616 GT:DP:GQ:MIN_DP:PL 0/0:35:76:35:0,76,992 -20_10037292_10066351 8617 . C . . END=8621 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1172 -20_10037292_10066351 8622 . A . . END=8622 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1142 -20_10037292_10066351 8623 . A . . END=8626 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1161 -20_10037292_10066351 8627 . T . . END=8627 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1107 -20_10037292_10066351 8628 . C . . END=8633 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,111,1183 -20_10037292_10066351 8634 . T . . END=8634 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1029 -20_10037292_10066351 8635 . G . . END=8638 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,101,1091 -20_10037292_10066351 8639 . C . . END=8640 GT:DP:GQ:MIN_DP:PL 0/0:39:87:38:0,87,1121 -20_10037292_10066351 8641 . A . . END=8646 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,102,1530 -20_10037292_10066351 8647 . T . . END=8647 GT:DP:GQ:MIN_DP:PL 0/0:38:85:38:0,85,1107 -20_10037292_10066351 8648 . T . . END=8648 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 8649 . T . . END=8649 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1060 -20_10037292_10066351 8650 . C . . END=8650 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1122 -20_10037292_10066351 8651 . T . . END=8652 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 8653 . C . . END=8654 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1051 -20_10037292_10066351 8655 . C . . END=8656 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 8657 . C . . END=8657 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,997 -20_10037292_10066351 8658 . C . . END=8658 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8659 . A . . END=8659 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8660 . G . . END=8660 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,990 -20_10037292_10066351 8661 . T . . END=8662 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1018 -20_10037292_10066351 8663 . A . . END=8667 GT:DP:GQ:MIN_DP:PL 0/0:38:93:36:0,93,1065 -20_10037292_10066351 8668 . A . . END=8679 GT:DP:GQ:MIN_DP:PL 0/0:32:82:31:0,82,918 -20_10037292_10066351 8680 . A . . END=8681 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 8682 . G . . END=8684 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8685 . T . . END=8685 GT:DP:GQ:MIN_DP:PL 0/0:29:70:29:0,70,762 -20_10037292_10066351 8686 . C . . END=8687 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8688 . G . . END=8688 GT:DP:GQ:MIN_DP:PL 0/0:32:61:32:0,61,872 -20_10037292_10066351 8689 . A . . END=8691 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,834 -20_10037292_10066351 8692 . G . . END=8698 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,868 -20_10037292_10066351 8699 . T . . END=8701 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8702 . T . . END=8703 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 8704 . T . . END=8704 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 8705 . T . . END=8705 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 8706 . G . . END=8706 GT:DP:GQ:MIN_DP:PL 0/0:35:77:35:0,77,957 -20_10037292_10066351 8707 . T . . END=8709 GT:DP:GQ:MIN_DP:PL 0/0:35:96:33:0,96,1440 -20_10037292_10066351 8710 . G . . END=8710 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,997 -20_10037292_10066351 8711 . C . . END=8712 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 8713 . C . . END=8714 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 8715 . T . . END=8718 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 8719 . T . . END=8721 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1045 -20_10037292_10066351 8722 . G . . END=8722 GT:DP:GQ:MIN_DP:PL 0/0:36:61:36:0,61,992 -20_10037292_10066351 8723 . G . . END=8727 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 8728 . G . . END=8728 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,990 -20_10037292_10066351 8729 . A . . END=8729 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 8730 . G . . END=8730 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,969 -20_10037292_10066351 8731 . T . . END=8734 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,913 -20_10037292_10066351 8735 . T . . END=8739 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,975 -20_10037292_10066351 8740 . C . . END=8740 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,927 -20_10037292_10066351 8741 . C . . END=8743 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,967 -20_10037292_10066351 8744 . A . . END=8744 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,923 -20_10037292_10066351 8745 . A . . END=8745 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,890 -20_10037292_10066351 8746 . C . . END=8748 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 8749 . C . . END=8750 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,994 -20_10037292_10066351 8751 . G . . END=8759 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,103,1064 -20_10037292_10066351 8760 . T . . END=8760 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1017 -20_10037292_10066351 8761 . T . . END=8762 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1096 -20_10037292_10066351 8763 . T . . END=8763 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1001 -20_10037292_10066351 8764 . A . . END=8765 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 8766 . A . . END=8766 GT:DP:GQ:MIN_DP:PL 0/0:38:89:38:0,89,1145 -20_10037292_10066351 8767 . G . . END=8767 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 8768 . G . . END=8768 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1150 -20_10037292_10066351 8769 . T . . END=8769 GT:DP:GQ:MIN_DP:PL 0/0:39:77:39:0,77,999 -20_10037292_10066351 8770 . G . . END=8773 GT:DP:GQ:MIN_DP:PL 0/0:37:91:36:0,91,1016 -20_10037292_10066351 8774 . G . . END=8774 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 8775 . C . . END=8775 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,998 -20_10037292_10066351 8776 . T . . END=8778 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,104,1072 -20_10037292_10066351 8779 . C . . END=8779 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1068 -20_10037292_10066351 8780 . A . . END=8781 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,113,1260 -20_10037292_10066351 8782 . G . . END=8782 GT:DP:GQ:MIN_DP:PL 0/0:42:59:42:0,59,1161 -20_10037292_10066351 8783 . A . . END=8787 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,117,1755 -20_10037292_10066351 8788 . G . . END=8788 GT:DP:GQ:MIN_DP:PL 0/0:41:75:41:0,75,1144 -20_10037292_10066351 8789 . T . . END=8789 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,937 -20_10037292_10066351 8790 . A . . END=8790 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,117,1755 -20_10037292_10066351 8791 . G . . END=8791 GT:DP:GQ:MIN_DP:PL 0/0:43:55:43:0,55,1222 -20_10037292_10066351 8792 . G . . END=8792 GT:DP:GQ:MIN_DP:PL 0/0:42:90:42:0,90,1152 -20_10037292_10066351 8793 . G . . END=8794 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,113,1282 -20_10037292_10066351 8795 . T . . END=8795 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1048 -20_10037292_10066351 8796 . T . . END=8800 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,99,1149 -20_10037292_10066351 8801 . T . . END=8802 GT:DP:GQ:MIN_DP:PL 0/0:44:92:44:0,92,1165 -20_10037292_10066351 8803 . C . . END=8804 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,109,1257 -20_10037292_10066351 8805 . C . . END=8805 GT:DP:GQ:MIN_DP:PL 0/0:43:80:43:0,80,1124 -20_10037292_10066351 8806 . C . . END=8813 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,101,1225 -20_10037292_10066351 8814 . G . . END=8814 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1205 -20_10037292_10066351 8815 . A . . END=8816 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,120,1800 -20_10037292_10066351 8817 . T . . END=8817 GT:DP:GQ:MIN_DP:PL 0/0:42:60:42:0,60,818 -20_10037292_10066351 8818 . T . . END=8818 GT:DP:GQ:MIN_DP:PL 0/0:41:81:41:0,81,952 -20_10037292_10066351 8819 . A . . END=8825 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,108,1206 -20_10037292_10066351 8826 . C . . END=8827 GT:DP:GQ:MIN_DP:PL 0/0:41:73:41:0,73,968 -20_10037292_10066351 8828 . G . . END=8832 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,104,1214 -20_10037292_10066351 8833 . G . . END=8833 GT:DP:GQ:MIN_DP:PL 0/0:39:79:39:0,79,1094 -20_10037292_10066351 8834 . G . . END=8834 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 8835 . C . . END=8835 GT:DP:GQ:MIN_DP:PL 0/0:40:77:40:0,77,982 -20_10037292_10066351 8836 . A . . END=8836 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,120,1800 -20_10037292_10066351 8837 . G . . END=8837 GT:DP:GQ:MIN_DP:PL 0/0:43:83:43:0,83,1211 -20_10037292_10066351 8838 . A . . END=8840 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,120,1800 -20_10037292_10066351 8841 . G . . END=8841 GT:DP:GQ:MIN_DP:PL 0/0:42:64:42:0,64,1114 -20_10037292_10066351 8842 . A . . END=8842 GT:DP:GQ:MIN_DP:PL 0/0:42:95:42:0,95,1237 -20_10037292_10066351 8843 . A . . END=8845 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,114,1710 -20_10037292_10066351 8846 . G . . END=8846 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1210 -20_10037292_10066351 8847 . G . . END=8851 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,100,1214 -20_10037292_10066351 8852 . G . . END=8852 GT:DP:GQ:MIN_DP:PL 0/0:41:88:41:0,88,1155 -20_10037292_10066351 8853 . G . . END=8853 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1143 -20_10037292_10066351 8854 . A . . END=8860 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,105,1575 -20_10037292_10066351 8861 . A . . END=8861 GT:DP:GQ:MIN_DP:PL 0/0:41:93:41:0,93,1254 -20_10037292_10066351 8862 . G . . END=8863 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,108,1620 -20_10037292_10066351 8864 . G . . END=8864 GT:DP:GQ:MIN_DP:PL 0/0:37:92:37:0,92,1056 -20_10037292_10066351 8865 . G . . END=8869 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1130 -20_10037292_10066351 8870 . G . . END=8870 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1042 -20_10037292_10066351 8871 . G . . END=8871 GT:DP:GQ:MIN_DP:PL 0/0:35:59:35:0,59,927 -20_10037292_10066351 8872 . A . . END=8880 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,99,1485 -20_10037292_10066351 8881 . A . . END=8885 GT:DP:GQ:MIN_DP:PL 0/0:38:81:37:0,81,1215 -20_10037292_10066351 8886 . AAGAAAGAAAG A, 951.03 . DP=30;ExcessHet=0.0000;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=108000,30 GT:AD:DP:GQ:PL:SB 1/1:0,22,0:22:67:965,67,0,965,67,965:0,0,20,2 -20_10037292_10066351 8897 . A . . END=8903 GT:DP:GQ:MIN_DP:PL 0/0:34:84:31:0,84,1260 -20_10037292_10066351 8904 . A . . END=8904 GT:DP:GQ:MIN_DP:PL 0/0:31:0:31:0,0,722 -20_10037292_10066351 8905 . A . . END=8905 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8906 . G . . END=8906 GT:DP:GQ:MIN_DP:PL 0/0:32:4:32:0,4,766 -20_10037292_10066351 8907 . A . . END=8908 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8909 . A . . END=8912 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,933 -20_10037292_10066351 8913 . A . . END=8913 GT:DP:GQ:MIN_DP:PL 0/0:31:82:31:0,82,920 -20_10037292_10066351 8914 . G . . END=8914 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,908 -20_10037292_10066351 8915 . A . . END=8916 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 8917 . A . . END=8917 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8918 . G . . END=8918 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,873 -20_10037292_10066351 8919 . A . . END=8920 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1215 -20_10037292_10066351 8921 . A . . END=8921 GT:DP:GQ:MIN_DP:PL 0/0:32:68:32:0,68,889 -20_10037292_10066351 8922 . G . . END=8928 GT:DP:GQ:MIN_DP:PL 0/0:32:75:32:0,75,1125 -20_10037292_10066351 8929 . G . . END=8929 GT:DP:GQ:MIN_DP:PL 0/0:31:67:31:0,67,862 -20_10037292_10066351 8930 . A . . END=8936 GT:DP:GQ:MIN_DP:PL 0/0:33:71:30:0,71,953 -20_10037292_10066351 8937 . G . . END=8937 GT:DP:GQ:MIN_DP:PL 0/0:31:33:31:0,33,805 -20_10037292_10066351 8938 . A . . END=8938 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 8939 . G . . END=8939 GT:DP:GQ:MIN_DP:PL 0/0:28:38:28:0,38,740 -20_10037292_10066351 8940 . A . . END=8941 GT:DP:GQ:MIN_DP:PL 0/0:28:75:28:0,75,1125 -20_10037292_10066351 8942 . A . . END=8942 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,1035 -20_10037292_10066351 8943 . G . . END=8943 GT:DP:GQ:MIN_DP:PL 0/0:28:36:28:0,36,696 -20_10037292_10066351 8944 . A . . END=8947 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,727 -20_10037292_10066351 8948 . G . . END=8948 GT:DP:GQ:MIN_DP:PL 0/0:27:50:27:0,50,740 -20_10037292_10066351 8949 . G . . END=8949 GT:DP:GQ:MIN_DP:PL 0/0:27:41:27:0,41,632 -20_10037292_10066351 8950 . A . . END=8951 GT:DP:GQ:MIN_DP:PL 0/0:27:69:26:0,69,1035 -20_10037292_10066351 8952 . A . . END=8953 GT:DP:GQ:MIN_DP:PL 0/0:25:59:25:0,59,671 -20_10037292_10066351 8954 . A . . END=8954 GT:DP:GQ:MIN_DP:PL 0/0:25:66:25:0,66,990 -20_10037292_10066351 8955 . G . . END=8955 GT:DP:GQ:MIN_DP:PL 0/0:25:49:25:0,49,649 -20_10037292_10066351 8956 . A . . END=8957 GT:DP:GQ:MIN_DP:PL 0/0:27:65:26:0,65,792 -20_10037292_10066351 8958 . A . . END=8958 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 8959 . G . . END=8959 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,823 -20_10037292_10066351 8960 . A . . END=8962 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8963 . G . . END=8963 GT:DP:GQ:MIN_DP:PL 0/0:28:51:28:0,51,765 -20_10037292_10066351 8964 . A . . END=8964 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 8965 . G . . END=8965 GT:DP:GQ:MIN_DP:PL 0/0:28:52:28:0,52,736 -20_10037292_10066351 8966 . A . . END=8967 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8968 . G . . END=8968 GT:DP:GQ:MIN_DP:PL 0/0:28:68:28:0,68,792 -20_10037292_10066351 8969 . G . . END=8969 GT:DP:GQ:MIN_DP:PL 0/0:28:25:28:0,25,733 -20_10037292_10066351 8970 . A . . END=8974 GT:DP:GQ:MIN_DP:PL 0/0:28:72:28:0,72,1080 -20_10037292_10066351 8975 . G . . END=8975 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,755 -20_10037292_10066351 8976 . A . . END=8976 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 8977 . G . . END=8977 GT:DP:GQ:MIN_DP:PL 0/0:29:54:29:0,54,794 -20_10037292_10066351 8978 . A . . END=8981 GT:DP:GQ:MIN_DP:PL 0/0:29:74:28:0,74,898 -20_10037292_10066351 8982 . A . . END=8982 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 8983 . G . . END=8983 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,858 -20_10037292_10066351 8984 . A . . END=8988 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 8989 . G . . END=8989 GT:DP:GQ:MIN_DP:PL 0/0:31:63:31:0,63,829 -20_10037292_10066351 8990 . A . . END=8992 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8993 . G . . END=8993 GT:DP:GQ:MIN_DP:PL 0/0:32:51:32:0,51,788 -20_10037292_10066351 8994 . A . . END=8994 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 8995 . G . . END=8995 GT:DP:GQ:MIN_DP:PL 0/0:32:64:32:0,64,844 -20_10037292_10066351 8996 . A . . END=8996 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 8997 . G . . END=8997 GT:DP:GQ:MIN_DP:PL 0/0:32:41:32:0,41,828 -20_10037292_10066351 8998 . A . . END=8998 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 8999 . G . . END=8999 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,719 -20_10037292_10066351 9000 . A . . END=9002 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 9003 . G . . END=9003 GT:DP:GQ:MIN_DP:PL 0/0:33:24:33:0,24,806 -20_10037292_10066351 9004 . A . . END=9006 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,1125 -20_10037292_10066351 9007 . G . . END=9007 GT:DP:GQ:MIN_DP:PL 0/0:34:32:34:0,32,867 -20_10037292_10066351 9008 . G . . END=9010 GT:DP:GQ:MIN_DP:PL 0/0:34:70:33:0,70,904 -20_10037292_10066351 9011 . G . . END=9011 GT:DP:GQ:MIN_DP:PL 0/0:34:48:34:0,48,883 -20_10037292_10066351 9012 . G . . END=9012 GT:DP:GQ:MIN_DP:PL 0/0:35:57:35:0,57,916 -20_10037292_10066351 9013 . A . . END=9014 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1215 -20_10037292_10066351 9015 . G . . END=9015 GT:DP:GQ:MIN_DP:PL 0/0:32:47:32:0,47,817 -20_10037292_10066351 9016 . G . . END=9018 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 9019 . G . . END=9019 GT:DP:GQ:MIN_DP:PL 0/0:31:17:31:0,17,656 -20_10037292_10066351 9020 . A . . END=9023 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,830 -20_10037292_10066351 9024 . A . . END=9024 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,908 -20_10037292_10066351 9025 . T . . END=9025 GT:DP:GQ:MIN_DP:PL 0/0:31:0:31:0,0,565 -20_10037292_10066351 9026 . G . . END=9026 GT:DP:GQ:MIN_DP:PL 0/0:31:61:31:0,61,793 -20_10037292_10066351 9027 . A . . END=9028 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,910 -20_10037292_10066351 9029 . G . . END=9029 GT:DP:GQ:MIN_DP:PL 0/0:31:35:31:0,35,751 -20_10037292_10066351 9030 . G . . END=9030 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,788 -20_10037292_10066351 9031 . G . . END=9031 GT:DP:GQ:MIN_DP:PL 0/0:31:48:31:0,48,740 -20_10037292_10066351 9032 . A . . END=9032 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,957 -20_10037292_10066351 9033 . G . . END=9033 GT:DP:GQ:MIN_DP:PL 0/0:31:7:31:0,7,679 -20_10037292_10066351 9034 . G . . END=9034 GT:DP:GQ:MIN_DP:PL 0/0:30:47:30:0,47,734 -20_10037292_10066351 9035 . A . . END=9035 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 9036 . A . . END=9036 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 9037 . G . . END=9037 GT:DP:GQ:MIN_DP:PL 0/0:31:18:31:0,18,704 -20_10037292_10066351 9038 . G . . END=9038 GT:DP:GQ:MIN_DP:PL 0/0:30:8:30:0,8,670 -20_10037292_10066351 9039 . A . . END=9043 GT:DP:GQ:MIN_DP:PL 0/0:32:81:30:0,81,1215 -20_10037292_10066351 9044 . G . . END=9044 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,924 -20_10037292_10066351 9045 . G . . END=9046 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9047 . G . . END=9047 GT:DP:GQ:MIN_DP:PL 0/0:28:62:28:0,62,781 -20_10037292_10066351 9048 . A . . END=9048 GT:DP:GQ:MIN_DP:PL 0/0:29:76:29:0,76,828 -20_10037292_10066351 9049 . C . . END=9049 GT:DP:GQ:MIN_DP:PL 0/0:29:59:29:0,59,696 -20_10037292_10066351 9050 . A . . END=9050 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 9051 . G . . END=9051 GT:DP:GQ:MIN_DP:PL 0/0:29:68:29:0,68,812 -20_10037292_10066351 9052 . G . . END=9052 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9053 . A . . END=9053 GT:DP:GQ:MIN_DP:PL 0/0:31:72:31:0,72,916 -20_10037292_10066351 9054 . A . . END=9054 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 9055 . G . . END=9055 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,853 -20_10037292_10066351 9056 . G . . END=9056 GT:DP:GQ:MIN_DP:PL 0/0:32:56:32:0,56,834 -20_10037292_10066351 9057 . A . . END=9058 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 9059 . G . . END=9059 GT:DP:GQ:MIN_DP:PL 0/0:35:49:35:0,49,882 -20_10037292_10066351 9060 . A . . END=9062 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 9063 . G . . END=9063 GT:DP:GQ:MIN_DP:PL 0/0:35:71:35:0,71,966 -20_10037292_10066351 9064 . A . . END=9066 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9067 . A . . END=9067 GT:DP:GQ:MIN_DP:PL 0/0:37:97:37:0,97,1111 -20_10037292_10066351 9068 . A . . END=9068 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,103,1210 -20_10037292_10066351 9069 . G . . END=9070 GT:DP:GQ:MIN_DP:PL 0/0:38:95:37:0,95,1130 -20_10037292_10066351 9071 . A . . END=9071 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9072 . G . . END=9072 GT:DP:GQ:MIN_DP:PL 0/0:39:72:39:0,72,1096 -20_10037292_10066351 9073 . A . . END=9076 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1575 -20_10037292_10066351 9077 . A . . END=9077 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1122 -20_10037292_10066351 9078 . A . . END=9078 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,102,1530 -20_10037292_10066351 9079 . G . . END=9079 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1129 -20_10037292_10066351 9080 . A . . END=9081 GT:DP:GQ:MIN_DP:PL 0/0:37:94:36:0,94,1155 -20_10037292_10066351 9082 . A . . END=9082 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9083 . G . . END=9084 GT:DP:GQ:MIN_DP:PL 0/0:38:97:37:0,97,1128 -20_10037292_10066351 9085 . G . . END=9086 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,104,1191 -20_10037292_10066351 9087 . A . . END=9087 GT:DP:GQ:MIN_DP:PL 0/0:41:96:41:0,96,1178 -20_10037292_10066351 9088 . A . . END=9089 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 9090 . A . . END=9090 GT:DP:GQ:MIN_DP:PL 0/0:40:75:40:0,75,1127 -20_10037292_10066351 9091 . A . . END=9093 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,114,1710 -20_10037292_10066351 9094 . G . . END=9094 GT:DP:GQ:MIN_DP:PL 0/0:40:70:40:0,70,1129 -20_10037292_10066351 9095 . A . . END=9095 GT:DP:GQ:MIN_DP:PL 0/0:40:87:40:0,87,1152 -20_10037292_10066351 9096 . A . . END=9097 GT:DP:GQ:MIN_DP:PL 0/0:40:73:40:0,73,1129 -20_10037292_10066351 9098 . G . . END=9099 GT:DP:GQ:MIN_DP:PL 0/0:40:88:39:0,88,1119 -20_10037292_10066351 9100 . A . . END=9100 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 9101 . A . . END=9102 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 -20_10037292_10066351 9103 . A . . END=9103 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1107 -20_10037292_10066351 9104 . A . . END=9109 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,99,1485 -20_10037292_10066351 9110 . G . . END=9110 GT:DP:GQ:MIN_DP:PL 0/0:37:84:37:0,84,1156 -20_10037292_10066351 9111 . A . . END=9111 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 9112 . A . . END=9112 GT:DP:GQ:MIN_DP:PL 0/0:37:59:37:0,59,1075 -20_10037292_10066351 9113 . G . . END=9115 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,101,1235 -20_10037292_10066351 9116 . A . . END=9116 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1139 -20_10037292_10066351 9117 . A . . END=9140 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1026 -20_10037292_10066351 9141 . A . . END=9151 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1091 -20_10037292_10066351 9152 . C . . END=9153 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 9154 . A . . END=9155 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9156 . A . . END=9156 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,954 -20_10037292_10066351 9157 . A . . END=9157 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 9158 . C . . END=9163 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,921 -20_10037292_10066351 9164 . C . . END=9164 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1007 -20_10037292_10066351 9165 . C . . END=9165 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,961 -20_10037292_10066351 9166 . T . . END=9168 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 9169 . C . . END=9169 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,934 -20_10037292_10066351 9170 . C . . END=9170 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 9171 . A . . END=9171 GT:DP:GQ:MIN_DP:PL 0/0:34:71:34:0,71,995 -20_10037292_10066351 9172 . T . . END=9174 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 9175 . A . . END=9175 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,940 -20_10037292_10066351 9176 . A . . END=9176 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1037 -20_10037292_10066351 9177 . T . . END=9177 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,1003 -20_10037292_10066351 9178 . G . . END=9181 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,871 -20_10037292_10066351 9182 . G . . END=9182 GT:DP:GQ:MIN_DP:PL 0/0:32:57:32:0,57,895 -20_10037292_10066351 9183 . A . . END=9184 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1006 -20_10037292_10066351 9185 . T . . END=9185 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1095 -20_10037292_10066351 9186 . T . . END=9186 GT:DP:GQ:MIN_DP:PL 0/0:35:70:35:0,70,1024 -20_10037292_10066351 9187 . T . . END=9188 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,102,1530 -20_10037292_10066351 9189 . T . . END=9189 GT:DP:GQ:MIN_DP:PL 0/0:37:93:37:0,93,1048 -20_10037292_10066351 9190 . C . . END=9193 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,105,1575 -20_10037292_10066351 9194 . A . . END=9194 GT:DP:GQ:MIN_DP:PL 0/0:36:95:36:0,95,1071 -20_10037292_10066351 9195 . C . . END=9196 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 9197 . C . . END=9197 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 9198 . A . . END=9206 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1485 -20_10037292_10066351 9207 . C . . END=9208 GT:DP:GQ:MIN_DP:PL 0/0:36:92:35:0,92,1103 -20_10037292_10066351 9209 . T . . END=9209 GT:DP:GQ:MIN_DP:PL 0/0:35:63:35:0,63,1038 -20_10037292_10066351 9210 . T . . END=9211 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 -20_10037292_10066351 9212 . A . . END=9214 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,1260 -20_10037292_10066351 9215 . T . . END=9219 GT:DP:GQ:MIN_DP:PL 0/0:34:78:32:0,78,1170 -20_10037292_10066351 9220 . C . . END=9222 GT:DP:GQ:MIN_DP:PL 0/0:32:81:29:0,81,1215 -20_10037292_10066351 9223 . C . . END=9224 GT:DP:GQ:MIN_DP:PL 0/0:30:75:29:0,75,1125 -20_10037292_10066351 9225 . A . . END=9227 GT:DP:GQ:MIN_DP:PL 0/0:29:63:27:0,63,945 -20_10037292_10066351 9228 . T . . END=9231 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,1080 -20_10037292_10066351 9232 . C . . END=9232 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,940 -20_10037292_10066351 9233 . C . . END=9236 GT:DP:GQ:MIN_DP:PL 0/0:29:75:26:0,75,832 -20_10037292_10066351 9237 . G . . END=9237 GT:DP:GQ:MIN_DP:PL 0/0:26:62:26:0,62,795 -20_10037292_10066351 9238 . C . . END=9241 GT:DP:GQ:MIN_DP:PL 0/0:27:80:27:0,80,780 -20_10037292_10066351 9242 . C . . END=9243 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,820 -20_10037292_10066351 9244 . C . . END=9244 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,798 -20_10037292_10066351 9245 . A . . END=9248 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,862 -20_10037292_10066351 9249 . G . . END=9249 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,874 -20_10037292_10066351 9250 . C . . END=9250 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,912 -20_10037292_10066351 9251 . A . . END=9254 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9255 . T . . END=9255 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,894 -20_10037292_10066351 9256 . C . . END=9257 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9258 . C . . END=9264 GT:DP:GQ:MIN_DP:PL 0/0:28:70:27:0,70,861 -20_10037292_10066351 9265 . A . . END=9265 GT:DP:GQ:MIN_DP:PL 0/0:27:52:27:0,52,775 -20_10037292_10066351 9266 . T . . END=9274 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 9275 . C . . END=9275 GT:DP:GQ:MIN_DP:PL 0/0:26:47:26:0,47,781 -20_10037292_10066351 9276 . A . . END=9282 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9283 . T . . END=9283 GT:DP:GQ:MIN_DP:PL 0/0:29:61:29:0,61,866 -20_10037292_10066351 9284 . C . . END=9284 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 9285 . T . . END=9286 GT:DP:GQ:MIN_DP:PL 0/0:29:74:29:0,74,888 -20_10037292_10066351 9287 . A . . END=9292 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 9293 . A . . END=9294 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,958 -20_10037292_10066351 9295 . T . . END=9299 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 9300 . T . . END=9300 GT:DP:GQ:MIN_DP:PL 0/0:32:74:32:0,74,931 -20_10037292_10066351 9301 . C . . END=9305 GT:DP:GQ:MIN_DP:PL 0/0:33:90:31:0,90,1350 -20_10037292_10066351 9306 . A . . END=9306 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,949 -20_10037292_10066351 9307 . A . . END=9308 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 9309 . C . . END=9309 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,886 -20_10037292_10066351 9310 . C . . END=9315 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,943 -20_10037292_10066351 9316 . A . . END=9316 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,941 -20_10037292_10066351 9317 . A . . END=9317 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,978 -20_10037292_10066351 9318 . A . . END=9318 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,959 -20_10037292_10066351 9319 . C . . END=9322 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,997 -20_10037292_10066351 9323 . T . . END=9323 GT:DP:GQ:MIN_DP:PL 0/0:31:48:31:0,48,899 -20_10037292_10066351 9324 . C . . END=9324 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1109 -20_10037292_10066351 9325 . T . . END=9329 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1099 -20_10037292_10066351 9330 . A . . END=9338 GT:DP:GQ:MIN_DP:PL 0/0:35:81:32:0,81,1215 -20_10037292_10066351 9339 . A . . END=9341 GT:DP:GQ:MIN_DP:PL 0/0:31:78:29:0,78,1170 -20_10037292_10066351 9342 . A . . END=9343 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 9344 . T . . END=9346 GT:DP:GQ:MIN_DP:PL 0/0:30:78:29:0,78,1170 -20_10037292_10066351 9347 . T . . END=9352 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260 -20_10037292_10066351 9353 . T . . END=9353 GT:DP:GQ:MIN_DP:PL 0/0:28:63:28:0,63,794 -20_10037292_10066351 9354 . T . . END=9360 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 9361 . G . . END=9364 GT:DP:GQ:MIN_DP:PL 0/0:29:71:27:0,71,893 -20_10037292_10066351 9365 . C . . END=9371 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,843 -20_10037292_10066351 9372 . T . . END=9372 GT:DP:GQ:MIN_DP:PL 0/0:29:63:29:0,63,824 -20_10037292_10066351 9373 . C . . END=9376 GT:DP:GQ:MIN_DP:PL 0/0:29:84:28:0,84,882 -20_10037292_10066351 9377 . A . . END=9377 GT:DP:GQ:MIN_DP:PL 0/0:31:69:31:0,69,880 -20_10037292_10066351 9378 . A . . END=9378 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 9379 . T . . END=9379 GT:DP:GQ:MIN_DP:PL 0/0:29:63:29:0,63,880 -20_10037292_10066351 9380 . T . . END=9380 GT:DP:GQ:MIN_DP:PL 0/0:30:56:30:0,56,834 -20_10037292_10066351 9381 . C . . END=9382 GT:DP:GQ:MIN_DP:PL 0/0:30:87:29:0,87,927 -20_10037292_10066351 9383 . C . . END=9383 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,991 -20_10037292_10066351 9384 . A . . END=9385 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,1005 -20_10037292_10066351 9386 . A . . END=9386 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 9387 . T . . END=9387 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,989 -20_10037292_10066351 9388 . C . . END=9390 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,979 -20_10037292_10066351 9391 . A . . END=9391 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,925 -20_10037292_10066351 9392 . C . . END=9392 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,969 -20_10037292_10066351 9393 . T . . END=9394 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9395 . T . . END=9396 GT:DP:GQ:MIN_DP:PL 0/0:35:84:34:0,84,967 -20_10037292_10066351 9397 . G . . END=9397 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 9398 . A . . END=9399 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 9400 . C . . END=9400 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,999 -20_10037292_10066351 9401 . T . . END=9410 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 9411 . A . . END=9411 GT:DP:GQ:MIN_DP:PL 0/0:33:76:33:0,76,993 -20_10037292_10066351 9412 . T . . END=9414 GT:DP:GQ:MIN_DP:PL 0/0:33:93:32:0,93,1395 -20_10037292_10066351 9415 . T . . END=9419 GT:DP:GQ:MIN_DP:PL 0/0:32:87:30:0,87,1305 -20_10037292_10066351 9420 . T . . END=9426 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 9427 . T . . END=9427 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,933 -20_10037292_10066351 9428 . A . . END=9437 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,902 -20_10037292_10066351 9438 . T . . END=9438 GT:DP:GQ:MIN_DP:PL 0/0:31:67:31:0,67,919 -20_10037292_10066351 9439 . T . . END=9439 GT:DP:GQ:MIN_DP:PL 0/0:33:39:33:0,39,897 -20_10037292_10066351 9440 . T . . END=9454 GT:DP:GQ:MIN_DP:PL 0/0:33:81:29:0,81,918 -20_10037292_10066351 9455 . G . . END=9455 GT:DP:GQ:MIN_DP:PL 0/0:29:73:29:0,73,898 -20_10037292_10066351 9456 . G . . END=9468 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,883 -20_10037292_10066351 9469 . T . . END=9478 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,1125 -20_10037292_10066351 9479 . A . . END=9479 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,801 -20_10037292_10066351 9480 . A . . END=9480 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 9481 . G . . END=9481 GT:DP:GQ:MIN_DP:PL 0/0:26:65:26:0,65,756 -20_10037292_10066351 9482 . C . . END=9484 GT:DP:GQ:MIN_DP:PL 0/0:27:72:24:0,72,748 -20_10037292_10066351 9485 . A . . END=9485 GT:DP:GQ:MIN_DP:PL 0/0:27:44:27:0,44,682 -20_10037292_10066351 9486 . A . . END=9486 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,746 -20_10037292_10066351 9487 . C . . END=9504 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,847 -20_10037292_10066351 9505 . A . . END=9505 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,804 -20_10037292_10066351 9506 . C . . END=9507 GT:DP:GQ:MIN_DP:PL 0/0:27:72:27:0,72,1080 -20_10037292_10066351 9508 . T . . END=9508 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,802 -20_10037292_10066351 9509 . G . . END=9511 GT:DP:GQ:MIN_DP:PL 0/0:26:72:24:0,72,758 -20_10037292_10066351 9512 . T . . END=9512 GT:DP:GQ:MIN_DP:PL 0/0:24:58:24:0,58,684 -20_10037292_10066351 9513 . C . . END=9526 GT:DP:GQ:MIN_DP:PL 0/0:26:60:25:0,60,900 -20_10037292_10066351 9527 . C . . END=9530 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 -20_10037292_10066351 9531 . C . . END=9534 GT:DP:GQ:MIN_DP:PL 0/0:27:69:23:0,69,651 -20_10037292_10066351 9535 . A . . END=9535 GT:DP:GQ:MIN_DP:PL 0/0:23:57:23:0,57,659 -20_10037292_10066351 9536 . T C, 148.64 . BaseQRankSum=-0.564;DP=21;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=75600,21;ReadPosRankSum=0.860 GT:AD:DP:GQ:PL:SB 0/1:14,7,0:21:99:156,0,353,197,374,571:3,11,5,2 -20_10037292_10066351 9537 . T . . END=9537 GT:DP:GQ:MIN_DP:PL 0/0:23:53:23:0,53,658 -20_10037292_10066351 9538 . C . . END=9538 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 9539 . A . . END=9539 GT:DP:GQ:MIN_DP:PL 0/0:24:22:24:0,22,564 -20_10037292_10066351 9540 . A . . END=9540 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -20_10037292_10066351 9541 . C . . END=9541 GT:DP:GQ:MIN_DP:PL 0/0:23:52:23:0,52,683 -20_10037292_10066351 9542 . T . . END=9542 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,683 -20_10037292_10066351 9543 . C . . END=9546 GT:DP:GQ:MIN_DP:PL 0/0:24:69:23:0,69,752 -20_10037292_10066351 9547 . T . . END=9548 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 9549 . A . . END=9549 GT:DP:GQ:MIN_DP:PL 0/0:27:65:27:0,65,760 -20_10037292_10066351 9550 . A . . END=9555 GT:DP:GQ:MIN_DP:PL 0/0:28:78:27:0,78,1170 -20_10037292_10066351 9556 . T . . END=9556 GT:DP:GQ:MIN_DP:PL 0/0:28:55:28:0,55,776 -20_10037292_10066351 9557 . A . . END=9557 GT:DP:GQ:MIN_DP:PL 0/0:27:47:27:0,47,778 -20_10037292_10066351 9558 . A . . END=9558 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,765 -20_10037292_10066351 9559 . A . . END=9561 GT:DP:GQ:MIN_DP:PL 0/0:27:70:26:0,70,832 -20_10037292_10066351 9562 . C . . END=9564 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 9565 . G . . END=9565 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 9566 . T . . END=9567 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 9568 . A . . END=9569 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 9570 . T . . END=9570 GT:DP:GQ:MIN_DP:PL 0/0:31:62:31:0,62,890 -20_10037292_10066351 9571 . C . . END=9578 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,983 -20_10037292_10066351 9579 . T . . END=9582 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,985 -20_10037292_10066351 9583 . A . . END=9583 GT:DP:GQ:MIN_DP:PL 0/0:32:63:32:0,63,921 -20_10037292_10066351 9584 . T . . END=9588 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,935 -20_10037292_10066351 9589 . A . . END=9589 GT:DP:GQ:MIN_DP:PL 0/0:32:77:32:0,77,898 -20_10037292_10066351 9590 . C . . END=9596 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,964 -20_10037292_10066351 9597 . C . . END=9597 GT:DP:GQ:MIN_DP:PL 0/0:31:74:31:0,74,881 -20_10037292_10066351 9598 . G . . END=9602 GT:DP:GQ:MIN_DP:PL 0/0:33:96:32:0,96,901 -20_10037292_10066351 9603 . A . . END=9627 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 9628 . A . . END=9628 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1440 -20_10037292_10066351 9629 . A . . END=9637 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1172 -20_10037292_10066351 9638 . A . . END=9638 GT:DP:GQ:MIN_DP:PL 0/0:36:68:36:0,68,946 -20_10037292_10066351 9639 . A . . END=9641 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 9642 . A . . END=9643 GT:DP:GQ:MIN_DP:PL 0/0:34:83:33:0,83,925 -20_10037292_10066351 9644 . T . . END=9648 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,102,1015 -20_10037292_10066351 9649 . T . . END=9649 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,980 -20_10037292_10066351 9650 . C . . END=9652 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1023 -20_10037292_10066351 9653 . T . . END=9653 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1058 -20_10037292_10066351 9654 . T . . END=9655 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,108,1065 -20_10037292_10066351 9656 . T . . END=9657 GT:DP:GQ:MIN_DP:PL 0/0:38:92:37:0,92,1061 -20_10037292_10066351 9658 . T . . END=9658 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1072 -20_10037292_10066351 9659 . T . . END=9659 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1070 -20_10037292_10066351 9660 . A . . END=9660 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 9661 . T . . END=9662 GT:DP:GQ:MIN_DP:PL 0/0:38:84:37:0,84,1058 -20_10037292_10066351 9663 . T . . END=9848 GT:DP:GQ:MIN_DP:PL 0/0:45:99:37:0,102,1151 -20_10037292_10066351 9849 . A . . END=9850 GT:DP:GQ:MIN_DP:PL 0/0:42:93:42:0,93,1083 -20_10037292_10066351 9851 . T . . END=9859 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,100,1156 -20_10037292_10066351 12912 . G . . END=12913 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440 -20_10037292_10066351 12914 . G . . END=12915 GT:DP:GQ:MIN_DP:PL 0/0:38:81:37:0,81,1160 -20_10037292_10066351 12916 . A . . END=12921 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 12922 . A . . END=12922 GT:DP:GQ:MIN_DP:PL 0/0:34:76:34:0,76,1008 -20_10037292_10066351 12923 . A . . END=12925 GT:DP:GQ:MIN_DP:PL 0/0:34:96:32:0,96,980 -20_10037292_10066351 12926 . C . . END=12926 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,899 -20_10037292_10066351 12927 . C . . END=12928 GT:DP:GQ:MIN_DP:PL 0/0:32:95:32:0,95,965 -20_10037292_10066351 12929 . G . . END=12929 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1119 -20_10037292_10066351 12930 . A . . END=12930 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 12931 . A . . END=12931 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,999 -20_10037292_10066351 12932 . A . . END=12932 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,994 -20_10037292_10066351 12933 . A . . END=12936 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 12937 . T . . END=12939 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 12940 . A . . END=12940 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 12941 . C . . END=12941 GT:DP:GQ:MIN_DP:PL 0/0:34:89:34:0,89,1007 -20_10037292_10066351 12942 . A . . END=12942 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,1056 -20_10037292_10066351 12943 . A . . END=12943 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1017 -20_10037292_10066351 12944 . A . . END=12946 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1350 -20_10037292_10066351 12947 . T . . END=12947 GT:DP:GQ:MIN_DP:PL 0/0:32:55:32:0,55,902 -20_10037292_10066351 12948 . G . . END=12953 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20_10037292_10066351 12954 . A . . END=12956 GT:DP:GQ:MIN_DP:PL 0/0:32:70:29:0,70,876 -20_10037292_10066351 12957 . A . . END=12957 GT:DP:GQ:MIN_DP:PL 0/0:29:58:29:0,58,804 -20_10037292_10066351 12958 . A . . END=12961 GT:DP:GQ:MIN_DP:PL 0/0:29:71:28:0,71,857 -20_10037292_10066351 12962 . G . . END=12967 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,840 -20_10037292_10066351 12968 . A . . END=12968 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,805 -20_10037292_10066351 12969 . G . . END=12969 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,914 -20_10037292_10066351 12970 . C . . END=12970 GT:DP:GQ:MIN_DP:PL 0/0:26:78:26:0,78,853 -20_10037292_10066351 12971 . T . . END=12972 GT:DP:GQ:MIN_DP:PL 0/0:27:68:27:0,68,758 -20_10037292_10066351 12973 . A . . END=12975 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 12976 . A . . END=12978 GT:DP:GQ:MIN_DP:PL 0/0:29:60:28:0,60,821 -20_10037292_10066351 12979 . A . . END=12979 GT:DP:GQ:MIN_DP:PL 0/0:29:57:29:0,57,846 -20_10037292_10066351 12980 . G . . END=12980 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 12981 . G . . END=12990 GT:DP:GQ:MIN_DP:PL 0/0:30:81:28:0,81,832 -20_10037292_10066351 12991 . A . . END=12993 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,1170 -20_10037292_10066351 12994 . A . . END=12994 GT:DP:GQ:MIN_DP:PL 0/0:32:66:32:0,66,884 -20_10037292_10066351 12995 . C . . END=12995 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,828 -20_10037292_10066351 12996 . G . . END=13013 GT:DP:GQ:MIN_DP:PL 0/0:31:81:28:0,81,857 -20_10037292_10066351 13014 . A . . END=13016 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,1125 -20_10037292_10066351 13017 . C . . END=13018 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13019 . C . . END=13019 GT:DP:GQ:MIN_DP:PL 0/0:30:59:30:0,59,851 -20_10037292_10066351 13020 . A . . END=13021 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 13022 . G . . END=13023 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 13024 . A . . END=13024 GT:DP:GQ:MIN_DP:PL 0/0:27:69:27:0,69,845 -20_10037292_10066351 13025 . A . . END=13026 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 13027 . A . . END=13027 GT:DP:GQ:MIN_DP:PL 0/0:26:66:26:0,66,815 -20_10037292_10066351 13028 . G . . END=13028 GT:DP:GQ:MIN_DP:PL 0/0:26:72:26:0,72,1080 -20_10037292_10066351 13029 . T . . END=13029 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,733 -20_10037292_10066351 13030 . A . . END=13034 GT:DP:GQ:MIN_DP:PL 0/0:28:72:27:0,72,845 -20_10037292_10066351 13035 . G . . END=13035 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,837 -20_10037292_10066351 13036 . T . . END=13036 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,788 -20_10037292_10066351 13037 . G . . END=13037 GT:DP:GQ:MIN_DP:PL 0/0:28:67:28:0,67,839 -20_10037292_10066351 13038 . T . . END=13040 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,833 -20_10037292_10066351 13041 . A . . END=13041 GT:DP:GQ:MIN_DP:PL 0/0:27:64:27:0,64,782 -20_10037292_10066351 13042 . T . . END=13051 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,835 -20_10037292_10066351 13052 . A . . END=13052 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13053 . G . . END=13054 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 13055 . T . . END=13055 GT:DP:GQ:MIN_DP:PL 0/0:37:80:37:0,80,1086 -20_10037292_10066351 13056 . C . . END=13057 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,108,1620 -20_10037292_10066351 13058 . A . . END=13058 GT:DP:GQ:MIN_DP:PL 0/0:40:69:40:0,69,1150 -20_10037292_10066351 13059 . T . . END=13059 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,111,1665 -20_10037292_10066351 13060 . T . . END=13060 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1152 -20_10037292_10066351 13061 . G . . END=13061 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 13062 . G . . END=13062 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1169 -20_10037292_10066351 13063 . T . . END=13063 GT:DP:GQ:MIN_DP:PL 0/0:39:91:39:0,91,1125 -20_10037292_10066351 13064 . T . . END=13064 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,108,1620 -20_10037292_10066351 13065 . T . . END=13065 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1139 -20_10037292_10066351 13066 . T . . END=13066 GT:DP:GQ:MIN_DP:PL 0/0:38:74:38:0,74,1124 -20_10037292_10066351 13067 . C . . END=13067 GT:DP:GQ:MIN_DP:PL 0/0:38:83:38:0,83,1143 -20_10037292_10066351 13068 . A . . END=13068 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1171 -20_10037292_10066351 13069 . C . . END=13069 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1174 -20_10037292_10066351 13070 . A . . END=13070 GT:DP:GQ:MIN_DP:PL 0/0:41:68:41:0,68,1170 -20_10037292_10066351 13071 . T . . END=13072 GT:DP:GQ:MIN_DP:PL 0/0:40:74:40:0,74,1159 -20_10037292_10066351 13073 . G . . END=13089 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,114,1259 -20_10037292_10066351 13090 . A . . END=13090 GT:DP:GQ:MIN_DP:PL 0/0:45:92:45:0,92,1316 -20_10037292_10066351 13091 . G . . END=13182 GT:DP:GQ:MIN_DP:PL 0/0:49:99:43:0,114,1309 -20_10037292_10066351 13183 . A . . END=13183 GT:DP:GQ:MIN_DP:PL 0/0:46:90:46:0,90,1291 -20_10037292_10066351 13184 . A . . END=13184 GT:DP:GQ:MIN_DP:PL 0/0:46:99:46:0,111,1665 -20_10037292_10066351 13185 . T A, 0 . BaseQRankSum=-0.574;DP=43;ExcessHet=0.0000;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=154800,43;ReadPosRankSum=2.040 GT:AD:DP:GQ:PL:SB 0/0:40,2,0:42:60:0,60,1194,120,1200,1259:20,20,2,0 -20_10037292_10066351 13186 . A . . END=13187 GT:DP:GQ:MIN_DP:PL 0/0:41:82:39:0,82,1220 -20_10037292_10066351 13188 . A . . END=13188 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1137 -20_10037292_10066351 13189 . A . . END=13189 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1126 -20_10037292_10066351 13190 . A . . END=13190 GT:DP:GQ:MIN_DP:PL 0/0:38:79:38:0,79,1147 -20_10037292_10066351 13191 . G . . END=13192 GT:DP:GQ:MIN_DP:PL 0/0:39:80:39:0,80,1118 -20_10037292_10066351 13193 . C . . END=13193 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1575 -20_10037292_10066351 13194 . A . . END=13195 GT:DP:GQ:MIN_DP:PL 0/0:39:83:38:0,83,1147 -20_10037292_10066351 13196 . T . . END=13196 GT:DP:GQ:MIN_DP:PL 0/0:39:67:39:0,67,1070 -20_10037292_10066351 13197 . A . . END=13197 GT:DP:GQ:MIN_DP:PL 0/0:39:96:39:0,96,1440 -20_10037292_10066351 13198 . T . . END=13199 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,105,1575 -20_10037292_10066351 13200 . T . . END=13200 GT:DP:GQ:MIN_DP:PL 0/0:42:72:42:0,72,1137 -20_10037292_10066351 13201 . T . . END=13205 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,101,1208 -20_10037292_10066351 13206 . C . . END=13206 GT:DP:GQ:MIN_DP:PL 0/0:39:94:39:0,94,1171 -20_10037292_10066351 13207 . T . . END=13207 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1156 -20_10037292_10066351 13208 . C . . END=13209 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 -20_10037292_10066351 13210 . A . . END=13210 GT:DP:GQ:MIN_DP:PL 0/0:39:83:39:0,83,1168 -20_10037292_10066351 13211 . G . . END=13211 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,108,1620 -20_10037292_10066351 13212 . C . . END=13212 GT:DP:GQ:MIN_DP:PL 0/0:39:84:39:0,84,1103 -20_10037292_10066351 13213 . T . . END=13214 GT:DP:GQ:MIN_DP:PL 0/0:42:90:41:0,90,1196 -20_10037292_10066351 13215 . T . . END=13215 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,110,1229 -20_10037292_10066351 13216 . T . . END=13216 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1208 -20_10037292_10066351 13217 . C . . END=13217 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,111,1665 -20_10037292_10066351 13218 . A . . END=13218 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1276 -20_10037292_10066351 13219 . A . . END=13219 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,111,1665 -20_10037292_10066351 13220 . G . . END=13220 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1192 -20_10037292_10066351 13221 . T . . END=13225 GT:DP:GQ:MIN_DP:PL 0/0:40:90:40:0,90,1157 -20_10037292_10066351 13226 . A . . END=13227 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,102,1530 -20_10037292_10066351 13228 . C . . END=13229 GT:DP:GQ:MIN_DP:PL 0/0:39:92:38:0,92,1150 -20_10037292_10066351 13230 . G . . END=13230 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,105,1177 -20_10037292_10066351 13231 . G . . END=13231 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1185 -20_10037292_10066351 13232 . A . . END=13232 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1172 -20_10037292_10066351 13233 . A . . END=13236 GT:DP:GQ:MIN_DP:PL 0/0:39:82:38:0,82,1118 -20_10037292_10066351 13237 . T . . END=13237 GT:DP:GQ:MIN_DP:PL 0/0:38:93:38:0,93,1395 -20_10037292_10066351 13238 . A . . END=13239 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1119 -20_10037292_10066351 13240 . C . . END=13240 GT:DP:GQ:MIN_DP:PL 0/0:38:90:38:0,90,1350 -20_10037292_10066351 13241 . C . . END=13242 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1089 -20_10037292_10066351 13243 . A . . END=13243 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 13244 . A . . END=13244 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1110 -20_10037292_10066351 13245 . G . . END=13245 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1076 -20_10037292_10066351 13246 . G . . END=13246 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1062 -20_10037292_10066351 13247 . A . . END=13249 GT:DP:GQ:MIN_DP:PL 0/0:33:93:33:0,93,1395 -20_10037292_10066351 13250 . T . . END=13251 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,1004 -20_10037292_10066351 13252 . A . . END=13252 GT:DP:GQ:MIN_DP:PL 0/0:34:82:34:0,82,1111 -20_10037292_10066351 13253 . G . . END=13254 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,1028 -20_10037292_10066351 13255 . T . . END=13255 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 13256 . T . . END=13256 GT:DP:GQ:MIN_DP:PL 0/0:34:79:34:0,79,1058 -20_10037292_10066351 13257 . T . . END=13257 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1036 -20_10037292_10066351 13258 . C . . END=13258 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,1048 -20_10037292_10066351 13259 . A . . END=13259 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1082 -20_10037292_10066351 13260 . C . . END=13260 GT:DP:GQ:MIN_DP:PL 0/0:35:72:35:0,72,1084 -20_10037292_10066351 13261 . A . . END=13262 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13263 . A . . END=13263 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,1018 -20_10037292_10066351 13264 . T . . END=13264 GT:DP:GQ:MIN_DP:PL 0/0:35:77:35:0,77,1107 -20_10037292_10066351 13265 . G . . END=13265 GT:DP:GQ:MIN_DP:PL 0/0:33:67:33:0,67,1009 -20_10037292_10066351 13266 . T . . END=13268 GT:DP:GQ:MIN_DP:PL 0/0:34:70:34:0,70,1039 -20_10037292_10066351 13269 . G . . END=13269 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13270 . A . . END=13271 GT:DP:GQ:MIN_DP:PL 0/0:34:76:34:0,76,1057 -20_10037292_10066351 13272 . C . . END=13272 GT:DP:GQ:MIN_DP:PL 0/0:34:69:34:0,69,1005 -20_10037292_10066351 13273 . A . . END=13275 GT:DP:GQ:MIN_DP:PL 0/0:36:91:36:0,91,1116 -20_10037292_10066351 13276 . A . . END=13276 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1156 -20_10037292_10066351 13277 . G . . END=13277 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 13278 . A . . END=13278 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1120 -20_10037292_10066351 13279 . C . . END=13279 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1119 -20_10037292_10066351 13280 . A . . END=13280 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1124 -20_10037292_10066351 13281 . T . . END=13281 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 13282 . C . . END=13282 GT:DP:GQ:MIN_DP:PL 0/0:36:58:36:0,58,1060 -20_10037292_10066351 13283 . T . . END=13285 GT:DP:GQ:MIN_DP:PL 0/0:36:75:36:0,75,1129 -20_10037292_10066351 13286 . T . . END=13286 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13287 . A . . END=13292 GT:DP:GQ:MIN_DP:PL 0/0:36:75:35:0,75,1083 -20_10037292_10066351 13293 . T . . END=13293 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1243 -20_10037292_10066351 13294 . G . . END=13294 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1142 -20_10037292_10066351 13295 . T . . END=13295 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 13296 . T . . END=13300 GT:DP:GQ:MIN_DP:PL 0/0:37:74:36:0,74,1111 -20_10037292_10066351 13301 . C . . END=13301 GT:DP:GQ:MIN_DP:PL 0/0:35:84:35:0,84,1260 -20_10037292_10066351 13302 . T . . END=13303 GT:DP:GQ:MIN_DP:PL 0/0:35:73:35:0,73,1126 -20_10037292_10066351 13304 . T . . END=13309 GT:DP:GQ:MIN_DP:PL 0/0:34:65:33:0,65,1022 -20_10037292_10066351 13310 . T . . END=13310 GT:DP:GQ:MIN_DP:PL 0/0:32:80:32:0,80,1010 -20_10037292_10066351 13311 . C . . END=13311 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,1004 -20_10037292_10066351 13312 . C . . END=13312 GT:DP:GQ:MIN_DP:PL 0/0:30:57:30:0,57,928 -20_10037292_10066351 13313 . T . . END=13314 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 13315 . T . . END=13317 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,960 -20_10037292_10066351 13318 . C . . END=13318 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1053 -20_10037292_10066351 13319 . T . . END=13319 GT:DP:GQ:MIN_DP:PL 0/0:33:81:33:0,81,1003 -20_10037292_10066351 13320 . T . . END=13320 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1013 -20_10037292_10066351 13321 . T . . END=13321 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,102,1100 -20_10037292_10066351 13322 . C . . END=13322 GT:DP:GQ:MIN_DP:PL 0/0:35:88:35:0,88,1089 -20_10037292_10066351 13323 . T . . END=13348 GT:DP:GQ:MIN_DP:PL 0/0:37:99:33:0,99,1043 -20_10037292_10066351 13349 . G . . END=13351 GT:DP:GQ:MIN_DP:PL 0/0:34:87:33:0,87,1073 -20_10037292_10066351 13352 . T . . END=13358 GT:DP:GQ:MIN_DP:PL 0/0:36:90:34:0,90,1350 -20_10037292_10066351 13359 . T . . END=13359 GT:DP:GQ:MIN_DP:PL 0/0:36:81:36:0,81,1077 -20_10037292_10066351 13360 . A . . END=13374 GT:DP:GQ:MIN_DP:PL 0/0:32:90:30:0,90,925 -20_10037292_10066351 13375 . C . . END=13377 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 13378 . T . . END=13378 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13379 . G . . END=13382 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1067 -20_10037292_10066351 13383 . T . . END=13383 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,1059 -20_10037292_10066351 13384 . G . . END=13385 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13386 . T . . END=13386 GT:DP:GQ:MIN_DP:PL 0/0:34:96:34:0,96,1440 -20_10037292_10066351 13387 . C . . END=13387 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1057 -20_10037292_10066351 13388 . T . . END=13395 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 13396 . C . . END=13396 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,1006 -20_10037292_10066351 13397 . A . . END=13404 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 13405 . T . . END=13406 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 13407 . T . . END=13408 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13409 . C . . END=13409 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,1023 -20_10037292_10066351 13410 . T . . END=13412 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13413 . T . . END=13416 GT:DP:GQ:MIN_DP:PL 0/0:32:81:31:0,81,1215 -20_10037292_10066351 13417 . T . . END=13417 GT:DP:GQ:MIN_DP:PL 0/0:30:63:30:0,63,940 -20_10037292_10066351 13418 . A . . END=13425 GT:DP:GQ:MIN_DP:PL 0/0:31:75:29:0,75,1125 -20_10037292_10066351 13426 . G . . END=13426 GT:DP:GQ:MIN_DP:PL 0/0:29:57:29:0,57,831 -20_10037292_10066351 13427 . A . . END=13452 GT:DP:GQ:MIN_DP:PL 0/0:25:62:23:0,62,762 -20_10037292_10066351 13453 . A . . END=13453 GT:DP:GQ:MIN_DP:PL 0/0:24:45:24:0,45,732 -20_10037292_10066351 13454 . T . . END=13455 GT:DP:GQ:MIN_DP:PL 0/0:25:66:25:0,66,990 -20_10037292_10066351 13456 . C . . END=13456 GT:DP:GQ:MIN_DP:PL 0/0:25:52:25:0,52,796 -20_10037292_10066351 13457 . T . . END=13466 GT:DP:GQ:MIN_DP:PL 0/0:24:60:22:0,60,900 -20_10037292_10066351 13467 . T . . END=13472 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,1080 -20_10037292_10066351 13473 . A . . END=13473 GT:DP:GQ:MIN_DP:PL 0/0:25:64:25:0,64,737 -20_10037292_10066351 13474 . A . . END=13478 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,849 -20_10037292_10066351 13479 . G . . END=13479 GT:DP:GQ:MIN_DP:PL 0/0:27:66:27:0,66,808 -20_10037292_10066351 13480 . G . . END=13489 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 -20_10037292_10066351 13490 . A . . END=13492 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,845 -20_10037292_10066351 13493 . A . . END=13493 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 -20_10037292_10066351 13494 . G . . END=13496 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20_10037292_10066351 13497 . A . . END=13508 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 13509 . C . . END=13510 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,875 -20_10037292_10066351 13511 . C . . END=13513 GT:DP:GQ:MIN_DP:PL 0/0:28:78:28:0,78,1170 -20_10037292_10066351 13514 . A . . END=13517 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 -20_10037292_10066351 13518 . T . . END=13518 GT:DP:GQ:MIN_DP:PL 0/0:30:76:30:0,76,931 -20_10037292_10066351 13519 . T . . END=13519 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 13520 . T . . END=13528 GT:DP:GQ:MIN_DP:PL 0/0:28:78:27:0,78,1170 -20_10037292_10066351 13529 . C . . END=13529 GT:DP:GQ:MIN_DP:PL 0/0:27:67:27:0,67,847 -20_10037292_10066351 13530 . T . . END=13534 GT:DP:GQ:MIN_DP:PL 0/0:26:75:26:0,75,862 -20_10037292_10066351 13535 . T . . END=13537 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 13538 . G . . END=13538 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,931 -20_10037292_10066351 13539 . G . . END=13539 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,893 -20_10037292_10066351 13540 . A . . END=13542 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,890 -20_10037292_10066351 13543 . C . . END=13543 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,891 -20_10037292_10066351 13544 . A . . END=13544 GT:DP:GQ:MIN_DP:PL 0/0:30:73:30:0,73,870 -20_10037292_10066351 13545 . C . . END=13545 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,818 -20_10037292_10066351 13546 . G . . END=13547 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,840 -20_10037292_10066351 13548 . T . . END=13548 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 -20_10037292_10066351 13549 . A . . END=13554 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,1350 -20_10037292_10066351 13555 . A . . END=13555 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13556 . T . . END=13556 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,969 -20_10037292_10066351 13557 . A . . END=13557 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1019 -20_10037292_10066351 13558 . C . . END=13558 GT:DP:GQ:MIN_DP:PL 0/0:33:85:33:0,85,940 -20_10037292_10066351 13559 . T . . END=13559 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1012 -20_10037292_10066351 13560 . C . . END=13560 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1034 -20_10037292_10066351 13561 . T . . END=13564 GT:DP:GQ:MIN_DP:PL 0/0:32:93:31:0,93,939 -20_10037292_10066351 13565 . C . . END=13565 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,961 -20_10037292_10066351 13566 . C . . END=13595 GT:DP:GQ:MIN_DP:PL 0/0:37:99:33:0,99,1037 -20_10037292_10066351 13596 . T . . END=13596 GT:DP:GQ:MIN_DP:PL 0/0:38:82:38:0,82,1054 -20_10037292_10066351 13597 . G . . END=13606 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 13607 . G . . END=13626 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,1003 -20_10037292_10066351 13627 . A . . END=13627 GT:DP:GQ:MIN_DP:PL 0/0:32:85:32:0,85,973 -20_10037292_10066351 13628 . A . . END=13629 GT:DP:GQ:MIN_DP:PL 0/0:32:93:32:0,93,1395 -20_10037292_10066351 13630 . T . . END=13630 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,886 -20_10037292_10066351 13631 . G . . END=13631 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13632 . A . . END=13633 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13634 . G . . END=13634 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13635 . T . . END=13635 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,888 -20_10037292_10066351 13636 . T . . END=13636 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13637 . T . . END=13637 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13638 . G . . END=13641 GT:DP:GQ:MIN_DP:PL 0/0:33:86:31:0,86,974 -20_10037292_10066351 13642 . T . . END=13643 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13644 . T . . END=13644 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,1305 -20_10037292_10066351 13645 . C . . END=13645 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13646 . C . . END=13648 GT:DP:GQ:MIN_DP:PL 0/0:33:87:32:0,87,1305 -20_10037292_10066351 13649 . G . . END=13649 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13650 . C . . END=13651 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13652 . G . . END=13654 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13655 . G . . END=13661 GT:DP:GQ:MIN_DP:PL 0/0:31:87:30:0,87,1305 -20_10037292_10066351 13662 . A . . END=13666 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,924 -20_10037292_10066351 13667 . A . . END=13667 GT:DP:GQ:MIN_DP:PL 0/0:29:87:29:0,87,879 -20_10037292_10066351 13668 . A . . END=13668 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,984 -20_10037292_10066351 13669 . G . . END=13669 GT:DP:GQ:MIN_DP:PL 0/0:30:74:30:0,74,931 -20_10037292_10066351 13670 . T . . END=13674 GT:DP:GQ:MIN_DP:PL 0/0:32:90:31:0,90,999 -20_10037292_10066351 13675 . G . . END=13675 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,1018 -20_10037292_10066351 13676 . G . . END=13692 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1081 -20_10037292_10066351 13693 . C . . END=13696 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 13697 . T . . END=13697 GT:DP:GQ:MIN_DP:PL 0/0:36:80:36:0,80,1068 -20_10037292_10066351 13698 . C . . END=13698 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,102,1530 -20_10037292_10066351 13699 . T . . END=13699 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1117 -20_10037292_10066351 13700 . G . . END=13706 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,945 -20_10037292_10066351 13707 . G . . END=13708 GT:DP:GQ:MIN_DP:PL 0/0:35:91:34:0,91,1046 -20_10037292_10066351 13709 . C . . END=13715 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,108,1620 -20_10037292_10066351 13716 . T . . END=13716 GT:DP:GQ:MIN_DP:PL 0/0:43:98:43:0,98,1230 -20_10037292_10066351 13717 . C . . END=13719 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,105,1575 -20_10037292_10066351 13720 . C . . END=13721 GT:DP:GQ:MIN_DP:PL 0/0:38:97:38:0,97,1111 -20_10037292_10066351 13722 . T . . END=13724 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,99,1174 -20_10037292_10066351 13725 . G . . END=13726 GT:DP:GQ:MIN_DP:PL 0/0:38:91:38:0,91,1107 -20_10037292_10066351 13727 . A . . END=13728 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 13729 . T . . END=13729 GT:DP:GQ:MIN_DP:PL 0/0:37:79:37:0,79,981 -20_10037292_10066351 13730 . A . . END=13735 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1056 -20_10037292_10066351 13736 . T . . END=13736 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,862 -20_10037292_10066351 13737 . A . . END=13737 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 -20_10037292_10066351 13738 . G . . END=13738 GT:DP:GQ:MIN_DP:PL 0/0:37:94:37:0,94,1134 -20_10037292_10066351 13739 . G . . END=13740 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 13741 . T . . END=13741 GT:DP:GQ:MIN_DP:PL 0/0:36:92:36:0,92,1018 -20_10037292_10066351 13742 . G . . END=13745 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 13746 . A . . END=13749 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 13750 . G . . END=13750 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,960 -20_10037292_10066351 13751 . C . . END=13756 GT:DP:GQ:MIN_DP:PL 0/0:34:93:32:0,93,964 -20_10037292_10066351 13757 . A . . END=13757 GT:DP:GQ:MIN_DP:PL 0/0:33:83:33:0,83,875 -20_10037292_10066351 13758 . A . . END=13758 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,973 -20_10037292_10066351 13759 . T . . END=13759 GT:DP:GQ:MIN_DP:PL 0/0:32:81:32:0,81,900 -20_10037292_10066351 13760 . G . . END=13761 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13762 . A . . END=13762 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,932 -20_10037292_10066351 13763 . C . . END=13763 GT:DP:GQ:MIN_DP:PL 0/0:33:53:33:0,53,879 -20_10037292_10066351 13764 . A . . END=13764 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13765 . T . . END=13765 GT:DP:GQ:MIN_DP:PL 0/0:33:30:33:0,30,748 -20_10037292_10066351 13766 . G . . END=13769 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13770 . G . . END=13770 GT:DP:GQ:MIN_DP:PL 0/0:34:68:34:0,68,975 -20_10037292_10066351 13771 . G . . END=13771 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13772 . T . . END=13773 GT:DP:GQ:MIN_DP:PL 0/0:34:75:34:0,75,924 -20_10037292_10066351 13774 . A . . END=13774 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,959 -20_10037292_10066351 13775 . T . . END=13775 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,970 -20_10037292_10066351 13776 . A . . END=13776 GT:DP:GQ:MIN_DP:PL 0/0:33:98:33:0,98,893 -20_10037292_10066351 13777 . A . . END=13777 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,923 -20_10037292_10066351 13778 . G . . END=13778 GT:DP:GQ:MIN_DP:PL 0/0:33:82:33:0,82,997 -20_10037292_10066351 13779 . C . . END=13788 GT:DP:GQ:MIN_DP:PL 0/0:33:91:32:0,91,956 -20_10037292_10066351 13789 . T . . END=13789 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 -20_10037292_10066351 13790 . T . . END=13800 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,962 -20_10037292_10066351 13801 . A . . END=13801 GT:DP:GQ:MIN_DP:PL 0/0:34:72:34:0,72,920 -20_10037292_10066351 13802 . C . . END=13802 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13803 . C . . END=13803 GT:DP:GQ:MIN_DP:PL 0/0:32:76:32:0,76,973 -20_10037292_10066351 13804 . A . . END=13804 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 13805 . G . . END=13806 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13807 . C . . END=13807 GT:DP:GQ:MIN_DP:PL 0/0:32:78:32:0,78,908 -20_10037292_10066351 13808 . T . . END=13808 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13809 . C . . END=13809 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,903 -20_10037292_10066351 13810 . A . . END=13810 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13811 . C . . END=13811 GT:DP:GQ:MIN_DP:PL 0/0:31:71:31:0,71,847 -20_10037292_10066351 13812 . T . . END=13814 GT:DP:GQ:MIN_DP:PL 0/0:30:84:29:0,84,1260 -20_10037292_10066351 13815 . C . . END=13815 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,877 -20_10037292_10066351 13816 . A . . END=13819 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 13820 . T . . END=13820 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,877 -20_10037292_10066351 13821 . T . . END=13821 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13822 . A . . END=13822 GT:DP:GQ:MIN_DP:PL 0/0:30:78:30:0,78,1170 -20_10037292_10066351 13823 . C . . END=13823 GT:DP:GQ:MIN_DP:PL 0/0:31:81:31:0,81,1215 -20_10037292_10066351 13824 . T . . END=13825 GT:DP:GQ:MIN_DP:PL 0/0:31:78:30:0,78,852 -20_10037292_10066351 13826 . C . . END=13830 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,881 -20_10037292_10066351 13831 . G . . END=13831 GT:DP:GQ:MIN_DP:PL 0/0:32:61:32:0,61,867 -20_10037292_10066351 13832 . T . . END=13832 GT:DP:GQ:MIN_DP:PL 0/0:31:58:31:0,58,806 -20_10037292_10066351 13833 . T . . END=13834 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,1350 -20_10037292_10066351 13835 . G . . END=13836 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 13837 . G . . END=13837 GT:DP:GQ:MIN_DP:PL 0/0:32:71:32:0,71,944 -20_10037292_10066351 13838 . A . . END=13845 GT:DP:GQ:MIN_DP:PL 0/0:32:80:31:0,80,959 -20_10037292_10066351 13846 . T . . END=13846 GT:DP:GQ:MIN_DP:PL 0/0:30:60:30:0,60,884 -20_10037292_10066351 13847 . T . . END=13847 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 -20_10037292_10066351 13848 . G . . END=13853 GT:DP:GQ:MIN_DP:PL 0/0:34:81:33:0,81,987 -20_10037292_10066351 13854 . A . . END=13857 GT:DP:GQ:MIN_DP:PL 0/0:33:78:32:0,78,1170 -20_10037292_10066351 13858 . A . . END=13858 GT:DP:GQ:MIN_DP:PL 0/0:35:84:35:0,84,1260 -20_10037292_10066351 13859 . T . . END=13859 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1350 -20_10037292_10066351 13860 . T . . END=13860 GT:DP:GQ:MIN_DP:PL 0/0:34:88:34:0,88,994 -20_10037292_10066351 13861 . C . . END=13863 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 13864 . A . . END=13864 GT:DP:GQ:MIN_DP:PL 0/0:34:77:34:0,77,978 -20_10037292_10066351 13865 . C . . END=13867 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13868 . T . . END=13868 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,998 -20_10037292_10066351 13869 . G . . END=13874 GT:DP:GQ:MIN_DP:PL 0/0:31:80:31:0,80,925 -20_10037292_10066351 13875 . A . . END=13875 GT:DP:GQ:MIN_DP:PL 0/0:31:79:31:0,79,910 -20_10037292_10066351 13876 . A . . END=13880 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -20_10037292_10066351 13881 . A . . END=13881 GT:DP:GQ:MIN_DP:PL 0/0:29:68:29:0,68,849 -20_10037292_10066351 13882 . C . . END=13883 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 13884 . T . . END=13885 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13886 . A . . END=13886 GT:DP:GQ:MIN_DP:PL 0/0:32:73:32:0,73,975 -20_10037292_10066351 13887 . G . . END=13892 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,896 -20_10037292_10066351 13893 . G . . END=13893 GT:DP:GQ:MIN_DP:PL 0/0:33:75:33:0,75,973 -20_10037292_10066351 13894 . T . . END=13895 GT:DP:GQ:MIN_DP:PL 0/0:33:90:32:0,90,1350 -20_10037292_10066351 13896 . A . . END=13896 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,960 -20_10037292_10066351 13897 . T . . END=13897 GT:DP:GQ:MIN_DP:PL 0/0:32:70:32:0,70,922 -20_10037292_10066351 13898 . T . . END=13898 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,87,971 -20_10037292_10066351 13899 . T . . END=13900 GT:DP:GQ:MIN_DP:PL 0/0:34:93:34:0,93,1395 -20_10037292_10066351 13901 . T . . END=13901 GT:DP:GQ:MIN_DP:PL 0/0:33:66:33:0,66,978 -20_10037292_10066351 13902 . A . . END=13902 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,924 -20_10037292_10066351 13903 . A . . END=13903 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13904 . A . . END=13905 GT:DP:GQ:MIN_DP:PL 0/0:32:87:31:0,87,1305 -20_10037292_10066351 13906 . A . . END=13906 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13907 . A . . END=13907 GT:DP:GQ:MIN_DP:PL 0/0:32:79:32:0,79,932 -20_10037292_10066351 13908 . A . . END=13909 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 13910 . G . . END=13912 GT:DP:GQ:MIN_DP:PL 0/0:32:83:32:0,83,950 -20_10037292_10066351 13913 . G . . END=13914 GT:DP:GQ:MIN_DP:PL 0/0:31:76:30:0,76,876 -20_10037292_10066351 13915 . T . . END=13915 GT:DP:GQ:MIN_DP:PL 0/0:32:82:32:0,82,967 -20_10037292_10066351 13916 . T . . END=13920 GT:DP:GQ:MIN_DP:PL 0/0:34:93:33:0,93,1395 -20_10037292_10066351 13921 . G . . END=13921 GT:DP:GQ:MIN_DP:PL 0/0:32:46:32:0,46,838 -20_10037292_10066351 13922 . G . . END=13922 GT:DP:GQ:MIN_DP:PL 0/0:33:69:33:0,69,895 -20_10037292_10066351 13923 . C . . END=13923 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13924 . T . . END=13924 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1032 -20_10037292_10066351 13925 . C . . END=13925 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,105,1575 -20_10037292_10066351 13926 . A . . END=13926 GT:DP:GQ:MIN_DP:PL 0/0:34:57:34:0,57,966 -20_10037292_10066351 13927 . C . . END=13927 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,104,1029 -20_10037292_10066351 13928 . A . . END=13928 GT:DP:GQ:MIN_DP:PL 0/0:34:84:34:0,84,1038 -20_10037292_10066351 13929 . G . . END=13929 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1017 -20_10037292_10066351 13930 . T . . END=13931 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,99,1485 -20_10037292_10066351 13932 . C . . END=13933 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1045 -20_10037292_10066351 13934 . G . . END=13934 GT:DP:GQ:MIN_DP:PL 0/0:35:83:35:0,83,1030 -20_10037292_10066351 13935 . C . . END=13936 GT:DP:GQ:MIN_DP:PL 0/0:35:90:35:0,90,1052 -20_10037292_10066351 13937 . G . . END=13937 GT:DP:GQ:MIN_DP:PL 0/0:35:77:35:0,77,1064 -20_10037292_10066351 13938 . G . . END=13938 GT:DP:GQ:MIN_DP:PL 0/0:35:89:35:0,89,991 -20_10037292_10066351 13939 . C . . END=13939 GT:DP:GQ:MIN_DP:PL 0/0:35:96:35:0,96,1440 -20_10037292_10066351 13940 . T . . END=13941 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 13942 . T . . END=13943 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 13944 . C . . END=13944 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,1007 -20_10037292_10066351 13945 . A . . END=13946 GT:DP:GQ:MIN_DP:PL 0/0:33:96:33:0,96,1440 -20_10037292_10066351 13947 . G . . END=13953 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,102,1156 -20_10037292_10066351 13954 . A . . END=13954 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1054 -20_10037292_10066351 13955 . G . . END=13958 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,102,1530 -20_10037292_10066351 13959 . C . . END=13959 GT:DP:GQ:MIN_DP:PL 0/0:39:92:39:0,92,1165 -20_10037292_10066351 13960 . T . . END=13965 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,101,1101 -20_10037292_10066351 13966 . C . . END=13966 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1180 -20_10037292_10066351 13967 . T . . END=13967 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1064 -20_10037292_10066351 13968 . C . . END=13969 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,111,1155 -20_10037292_10066351 13970 . G . . END=13970 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1159 -20_10037292_10066351 13971 . G . . END=13971 GT:DP:GQ:MIN_DP:PL 0/0:37:82:37:0,82,1061 -20_10037292_10066351 13972 . G . . END=13972 GT:DP:GQ:MIN_DP:PL 0/0:36:90:36:0,90,1094 -20_10037292_10066351 13973 . G . . END=13975 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,105,1575 -20_10037292_10066351 13976 . A . . END=13976 GT:DP:GQ:MIN_DP:PL 0/0:39:93:39:0,93,1112 -20_10037292_10066351 13977 . C . . END=13979 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,108,1620 -20_10037292_10066351 13980 . C . . END=13980 GT:DP:GQ:MIN_DP:PL 0/0:39:87:39:0,87,1102 -20_10037292_10066351 13981 . A . . END=13985 GT:DP:GQ:MIN_DP:PL 0/0:38:99:36:0,102,1530 -20_10037292_10066351 13986 . G . . END=13987 GT:DP:GQ:MIN_DP:PL 0/0:37:94:36:0,94,1097 -20_10037292_10066351 13988 . T . . END=13988 GT:DP:GQ:MIN_DP:PL 0/0:37:88:37:0,88,1106 -20_10037292_10066351 13989 . T . . END=13995 GT:DP:GQ:MIN_DP:PL 0/0:35:92:34:0,92,1082 -20_10037292_10066351 13996 . A . . END=13999 GT:DP:GQ:MIN_DP:PL 0/0:37:99:34:0,102,1029 -20_10037292_10066351 14000 . C . . END=14004 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1395 -20_10037292_10066351 14005 . G . . END=14005 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,99,1485 -20_10037292_10066351 14006 . G . . END=14006 GT:DP:GQ:MIN_DP:PL 0/0:38:70:38:0,70,1092 -20_10037292_10066351 14007 . C . . END=14007 GT:DP:GQ:MIN_DP:PL 0/0:38:98:38:0,98,1050 -20_10037292_10066351 14008 . A . . END=14010 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1485 -20_10037292_10066351 14011 . G . . END=14011 GT:DP:GQ:MIN_DP:PL 0/0:33:65:33:0,65,969 -20_10037292_10066351 14012 . G . . END=14012 GT:DP:GQ:MIN_DP:PL 0/0:33:99:33:0,99,1016 -20_10037292_10066351 14013 . G . . END=14014 GT:DP:GQ:MIN_DP:PL 0/0:34:85:34:0,85,962 -20_10037292_10066351 14015 . C . . END=14015 GT:DP:GQ:MIN_DP:PL 0/0:35:61:35:0,61,980 -20_10037292_10066351 14016 . A . . END=14016 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,108,1160 -20_10037292_10066351 14017 . G . . END=14017 GT:DP:GQ:MIN_DP:PL 0/0:36:93:36:0,93,1129 -20_10037292_10066351 14018 . C . . END=14018 GT:DP:GQ:MIN_DP:PL 0/0:35:99:35:0,104,884 -20_10037292_10066351 14019 . G . . END=14019 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1038 -20_10037292_10066351 14020 . A . . END=14020 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,114,1158 -20_10037292_10066351 14021 . G . . END=14022 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1108 -20_10037292_10066351 14023 . C . . END=14026 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,100,1138 -20_10037292_10066351 14027 . T . . END=14027 GT:DP:GQ:MIN_DP:PL 0/0:38:84:38:0,84,1053 -20_10037292_10066351 14028 . C . . END=14030 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,101,1155 -20_10037292_10066351 14031 . G . . END=14031 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1034 -20_10037292_10066351 14032 . G . . END=14042 GT:DP:GQ:MIN_DP:PL 0/0:43:99:38:0,102,1197 -20_10037292_10066351 14043 . A . . END=14043 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1196 -20_10037292_10066351 14044 . A . . END=14044 GT:DP:GQ:MIN_DP:PL 0/0:42:99:42:0,117,1755 -20_10037292_10066351 14045 . G . . END=14045 GT:DP:GQ:MIN_DP:PL 0/0:42:98:42:0,98,1338 -20_10037292_10066351 14046 . A . . END=14047 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,117,1755 -20_10037292_10066351 14048 . G . . END=14048 GT:DP:GQ:MIN_DP:PL 0/0:41:98:41:0,98,1245 -20_10037292_10066351 14049 . A . . END=14049 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,117,1755 -20_10037292_10066351 14050 . G . . END=14050 GT:DP:GQ:MIN_DP:PL 0/0:39:74:39:0,74,1093 -20_10037292_10066351 14051 . A . . END=14051 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,117,1234 -20_10037292_10066351 14052 . G . . END=14052 GT:DP:GQ:MIN_DP:PL 0/0:40:88:40:0,88,1192 -20_10037292_10066351 14053 . A . . END=14060 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,107,1225 -20_10037292_10066351 14061 . G . . END=14062 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1200 -20_10037292_10066351 14063 . G . . END=14066 GT:DP:GQ:MIN_DP:PL 0/0:43:99:41:0,102,1263 -20_10037292_10066351 14067 . C . . END=14067 GT:DP:GQ:MIN_DP:PL 0/0:40:93:40:0,93,1199 -20_10037292_10066351 14068 . C . . END=14172 GT:DP:GQ:MIN_DP:PL 0/0:45:99:38:0,99,1117 -20_10037292_10066351 14173 . T . . END=14173 GT:DP:GQ:MIN_DP:PL 0/0:45:78:45:0,78,1309 -20_10037292_10066351 14174 . C . . END=14190 GT:DP:GQ:MIN_DP:PL 0/0:45:99:38:0,108,1227 -20_10037292_10066351 14191 . C . . END=14191 GT:DP:GQ:MIN_DP:PL 0/0:38:65:38:0,65,1134 -20_10037292_10066351 14192 . T . . END=14198 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1137 -20_10037292_10066351 14199 . A . . END=14199 GT:DP:GQ:MIN_DP:PL 0/0:39:72:39:0,72,1156 -20_10037292_10066351 14200 . C . . END=14212 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1266 -20_10037292_10066351 14213 . G . . END=14213 GT:DP:GQ:MIN_DP:PL 0/0:37:91:37:0,91,1138 -20_10037292_10066351 14214 . T . . END=14214 GT:DP:GQ:MIN_DP:PL 0/0:36:76:36:0,76,1093 -20_10037292_10066351 14215 . G . . END=14216 GT:DP:GQ:MIN_DP:PL 0/0:36:99:36:0,99,1485 -20_10037292_10066351 14217 . T . . END=14221 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395 -20_10037292_10066351 14222 . G . . END=14228 GT:DP:GQ:MIN_DP:PL 0/0:36:99:34:0,99,1069 -20_10037292_10066351 14229 . C . . END=14229 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1031 -20_10037292_10066351 14230 . A . . END=14238 GT:DP:GQ:MIN_DP:PL 0/0:35:99:33:0,99,1036 -20_10037292_10066351 14239 . T . . END=14239 GT:DP:GQ:MIN_DP:PL 0/0:35:87:35:0,87,1067 -20_10037292_10066351 14240 . T . . END=14243 GT:DP:GQ:MIN_DP:PL 0/0:36:99:33:0,99,1029 -20_10037292_10066351 14244 . A . . END=14244 GT:DP:GQ:MIN_DP:PL 0/0:35:79:35:0,79,1043 -20_10037292_10066351 14245 . T . . END=14246 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1038 -20_10037292_10066351 14247 . A . . END=14249 GT:DP:GQ:MIN_DP:PL 0/0:34:90:34:0,90,1052 -20_10037292_10066351 14250 . T . . END=14250 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,995 -20_10037292_10066351 14251 . T . . END=14253 GT:DP:GQ:MIN_DP:PL 0/0:35:90:34:0,90,1350 -20_10037292_10066351 14254 . G . . END=14254 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,1260 -20_10037292_10066351 14255 . G . . END=14259 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1015 -20_10037292_10066351 14260 . G . . END=14260 GT:DP:GQ:MIN_DP:PL 0/0:32:61:32:0,61,918 -20_10037292_10066351 14261 . A . . END=14261 GT:DP:GQ:MIN_DP:PL 0/0:33:78:33:0,78,1170 -20_10037292_10066351 14262 . C . . END=14266 GT:DP:GQ:MIN_DP:PL 0/0:32:81:29:0,81,1215 -20_10037292_10066351 14267 . A . . END=14268 GT:DP:GQ:MIN_DP:PL 0/0:29:72:29:0,72,882 -20_10037292_10066351 14269 . C . . END=14269 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,828 -20_10037292_10066351 14270 . C . . END=14273 GT:DP:GQ:MIN_DP:PL 0/0:28:75:27:0,75,1125 -20_10037292_10066351 14274 . C . . END=14274 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 14275 . C . . END=14277 GT:DP:GQ:MIN_DP:PL 0/0:30:72:30:0,72,1080 -20_10037292_10066351 14278 . A . . END=14282 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,81,1215 -20_10037292_10066351 14283 . A . . END=14283 GT:DP:GQ:MIN_DP:PL 0/0:30:58:30:0,58,834 -20_10037292_10066351 14284 . A . . END=14286 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,900 -20_10037292_10066351 14287 . T . . END=14288 GT:DP:GQ:MIN_DP:PL 0/0:27:75:27:0,75,1125 -20_10037292_10066351 14289 . A . . END=14289 GT:DP:GQ:MIN_DP:PL 0/0:27:55:27:0,55,782 -20_10037292_10066351 14290 . T . . END=14291 GT:DP:GQ:MIN_DP:PL 0/0:29:72:26:0,72,945 -20_10037292_10066351 14292 . G . . END=14294 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 -20_10037292_10066351 14295 . T . . END=14295 GT:DP:GQ:MIN_DP:PL 0/0:31:35:31:0,35,906 -20_10037292_10066351 14296 . A . . END=14303 GT:DP:GQ:MIN_DP:PL 0/0:32:74:30:0,74,999 -20_10037292_10066351 14304 . C . . END=14309 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,909 -20_10037292_10066351 14310 . A . . END=14310 GT:DP:GQ:MIN_DP:PL 0/0:28:70:28:0,70,859 -20_10037292_10066351 14311 . A . . END=14319 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,942 -20_10037292_10066351 14320 . C . . END=14321 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,954 -20_10037292_10066351 14322 . A . . END=14326 GT:DP:GQ:MIN_DP:PL 0/0:31:84:31:0,84,1260 -20_10037292_10066351 14327 . G . . END=14327 GT:DP:GQ:MIN_DP:PL 0/0:31:32:31:0,32,833 -20_10037292_10066351 14328 . C . . END=14328 GT:DP:GQ:MIN_DP:PL 0/0:32:87:32:0,87,1305 -20_10037292_10066351 14329 . A . . END=14329 GT:DP:GQ:MIN_DP:PL 0/0:33:72:33:0,72,1013 -20_10037292_10066351 14330 . C . . END=14333 GT:DP:GQ:MIN_DP:PL 0/0:34:93:32:0,93,1033 -20_10037292_10066351 14334 . A . . END=14334 GT:DP:GQ:MIN_DP:PL 0/0:33:84:33:0,84,955 -20_10037292_10066351 14335 . T . . END=14335 GT:DP:GQ:MIN_DP:PL 0/0:33:77:33:0,77,965 -20_10037292_10066351 14336 . G . . END=14339 GT:DP:GQ:MIN_DP:PL 0/0:34:99:33:0,99,1019 -20_10037292_10066351 14340 . T . . END=14340 GT:DP:GQ:MIN_DP:PL 0/0:33:68:33:0,68,976 -20_10037292_10066351 14341 . A . . END=14350 GT:DP:GQ:MIN_DP:PL 0/0:40:99:34:0,102,1084 -20_10037292_10066351 14351 . G . . END=14351 GT:DP:GQ:MIN_DP:PL 0/0:40:95:40:0,95,1166 -20_10037292_10066351 14352 . G . . END=14352 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,120,1202 -20_10037292_10066351 14353 . T . . END=14353 GT:DP:GQ:MIN_DP:PL 0/0:40:67:40:0,67,1126 -20_10037292_10066351 14354 . T . . END=14363 GT:DP:GQ:MIN_DP:PL 0/0:41:99:40:0,114,1710 -20_10037292_10066351 14364 . C . . END=14364 GT:DP:GQ:MIN_DP:PL 0/0:41:46:41:0,46,1080 -20_10037292_10066351 14365 . A . . END=14370 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,111,1665 -20_10037292_10066351 14371 . G . . END=14371 GT:DP:GQ:MIN_DP:PL 0/0:43:97:43:0,97,1319 -20_10037292_10066351 14372 . C . . END=14372 GT:DP:GQ:MIN_DP:PL 0/0:44:65:44:0,65,1169 -20_10037292_10066351 14373 . A . . END=14373 GT:DP:GQ:MIN_DP:PL 0/0:42:49:42:0,49,1182 -20_10037292_10066351 14374 . T . . END=14445 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,99,1113 -20_10037292_10066351 14446 . C . . END=14452 GT:DP:GQ:MIN_DP:PL 0/0:35:96:34:0,96,1440 -20_10037292_10066351 14453 . C . . END=14455 GT:DP:GQ:MIN_DP:PL 0/0:35:99:34:0,99,1485 -20_10037292_10066351 14456 . T . . END=14457 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14458 . A . . END=14466 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485 -20_10037292_10066351 14467 . T . . END=14467 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 14468 . A . . END=14468 GT:DP:GQ:MIN_DP:PL 0/0:34:47:34:0,47,924 -20_10037292_10066351 14469 . C . . END=14473 GT:DP:GQ:MIN_DP:PL 0/0:35:93:34:0,93,1395 -20_10037292_10066351 14474 . A . . END=14480 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,99,1485 -20_10037292_10066351 14481 . A . . END=14481 GT:DP:GQ:MIN_DP:PL 0/0:38:78:38:0,78,1121 -20_10037292_10066351 14482 . T . . END=14483 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,102,1530 -20_10037292_10066351 14484 . A . . END=14485 GT:DP:GQ:MIN_DP:PL 0/0:40:93:39:0,93,1395 -20_10037292_10066351 14486 . A . . END=14486 GT:DP:GQ:MIN_DP:PL 0/0:43:99:43:0,105,1575 -20_10037292_10066351 14487 . C . . END=14487 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1206 -20_10037292_10066351 14488 . A . . END=14488 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,108,1620 -20_10037292_10066351 14489 . T . . END=14489 GT:DP:GQ:MIN_DP:PL 0/0:41:91:41:0,91,1263 -20_10037292_10066351 14490 . G . . END=14499 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,100,1154 -20_10037292_10066351 14500 . G . . END=14501 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1171 -20_10037292_10066351 14502 . C . . END=14505 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -20_10037292_10066351 14506 . C . . END=14506 GT:DP:GQ:MIN_DP:PL 0/0:39:98:39:0,98,1092 -20_10037292_10066351 14507 . G . . END=14511 GT:DP:GQ:MIN_DP:PL 0/0:39:99:38:0,105,1217 -20_10037292_10066351 14512 . T . . END=14512 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1193 -20_10037292_10066351 14513 . A . . END=14515 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,105,1575 -20_10037292_10066351 14516 . T . . END=14516 GT:DP:GQ:MIN_DP:PL 0/0:41:97:41:0,97,1234 -20_10037292_10066351 14517 . C . . END=14522 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,108,1620 -20_10037292_10066351 14523 . T . . END=14523 GT:DP:GQ:MIN_DP:PL 0/0:41:44:41:0,44,1133 -20_10037292_10066351 14524 . T . . END=14524 GT:DP:GQ:MIN_DP:PL 0/0:41:88:41:0,88,1204 -20_10037292_10066351 14525 . T . . END=14527 GT:DP:GQ:MIN_DP:PL 0/0:42:99:41:0,114,1354 -20_10037292_10066351 14528 . T . . END=14528 GT:DP:GQ:MIN_DP:PL 0/0:42:80:42:0,80,1203 -20_10037292_10066351 14529 . T . . END=14539 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,99,1258 -20_10037292_10066351 14540 . G . . END=14540 GT:DP:GQ:MIN_DP:PL 0/0:43:62:43:0,62,1280 -20_10037292_10066351 14541 . G . . END=14541 GT:DP:GQ:MIN_DP:PL 0/0:44:89:44:0,89,1287 -20_10037292_10066351 14542 . T . . END=14556 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,100,1290 -20_10037292_10066351 14557 . T . . END=14557 GT:DP:GQ:MIN_DP:PL 0/0:42:92:42:0,92,1329 -20_10037292_10066351 14558 . C . . END=14560 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,115,1319 -20_10037292_10066351 14561 . A . . END=14562 GT:DP:GQ:MIN_DP:PL 0/0:44:90:43:0,90,1314 -20_10037292_10066351 14563 . A . . END=14569 GT:DP:GQ:MIN_DP:PL 0/0:44:99:43:0,115,1304 -20_10037292_10066351 14570 . C . . END=14570 GT:DP:GQ:MIN_DP:PL 0/0:43:79:43:0,79,1226 -20_10037292_10066351 14571 . A . . END=14595 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,102,1217 -20_10037292_10066351 14596 . C . . END=14596 GT:DP:GQ:MIN_DP:PL 0/0:40:50:40:0,50,1165 -20_10037292_10066351 14597 . A . . END=14603 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,103,1231 -20_10037292_10066351 14604 . C . . END=14604 GT:DP:GQ:MIN_DP:PL 0/0:39:95:39:0,95,1249 -20_10037292_10066351 14605 . T . . END=14609 GT:DP:GQ:MIN_DP:PL 0/0:38:99:37:0,102,1250 -20_10037292_10066351 14610 . A . . END=14610 GT:DP:GQ:MIN_DP:PL 0/0:37:98:37:0,98,1166 -20_10037292_10066351 14611 . C . . END=14611 GT:DP:GQ:MIN_DP:PL 0/0:37:78:37:0,78,1128 -20_10037292_10066351 14612 . A . . END=14612 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 -20_10037292_10066351 14613 . T . . END=14615 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1133 -20_10037292_10066351 14616 . C . . END=14616 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1152 -20_10037292_10066351 14617 . T . . END=14619 GT:DP:GQ:MIN_DP:PL 0/0:36:94:36:0,94,1134 -20_10037292_10066351 14620 . T . . END=14620 GT:DP:GQ:MIN_DP:PL 0/0:36:78:36:0,78,1075 -20_10037292_10066351 14621 . C . . END=14622 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1111 -20_10037292_10066351 14623 . C . . END=14623 GT:DP:GQ:MIN_DP:PL 0/0:37:81:37:0,81,1154 -20_10037292_10066351 14624 . C . . END=14624 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 -20_10037292_10066351 14625 . T . . END=14636 GT:DP:GQ:MIN_DP:PL 0/0:34:81:31:0,81,1132 -20_10037292_10066351 14637 . A . . END=14638 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 -20_10037292_10066351 14639 . T . . END=14644 GT:DP:GQ:MIN_DP:PL 0/0:29:81:28:0,81,1215 -20_10037292_10066351 14645 . G . . END=14655 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,825 -20_10037292_10066351 14656 . C . . END=14665 GT:DP:GQ:MIN_DP:PL 0/0:26:63:26:0,63,945 -20_10037292_10066351 14666 . A . . END=14666 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,659 -20_10037292_10066351 14667 . T . . END=14668 GT:DP:GQ:MIN_DP:PL 0/0:24:66:23:0,66,990 -20_10037292_10066351 14669 . T . . END=14672 GT:DP:GQ:MIN_DP:PL 0/0:23:57:21:0,57,702 -20_10037292_10066351 14673 . T . . END=14673 GT:DP:GQ:MIN_DP:PL 0/0:23:43:23:0,43,645 -20_10037292_10066351 14674 . G . . END=14692 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,776 -20_10037292_10066351 14693 . T . . END=14697 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,718 -20_10037292_10066351 14698 . A . . END=14698 GT:DP:GQ:MIN_DP:PL 0/0:28:84:28:0,84,913 -20_10037292_10066351 14699 . T . . END=14699 GT:DP:GQ:MIN_DP:PL 0/0:28:71:28:0,71,850 -20_10037292_10066351 14700 . A . . END=14703 GT:DP:GQ:MIN_DP:PL 0/0:31:90:30:0,90,927 -20_10037292_10066351 14704 . A . . END=14704 GT:DP:GQ:MIN_DP:PL 0/0:31:66:31:0,66,939 -20_10037292_10066351 14705 . A . . END=14712 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,90,954 -20_10037292_10066351 14713 . T . . END=14713 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,944 -20_10037292_10066351 14714 . T . . END=14714 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 14715 . A . . END=14715 GT:DP:GQ:MIN_DP:PL 0/0:31:73:31:0,73,932 -20_10037292_10066351 14716 . C . . END=14722 GT:DP:GQ:MIN_DP:PL 0/0:31:84:30:0,84,1260 -20_10037292_10066351 14723 . T . . END=14723 GT:DP:GQ:MIN_DP:PL 0/0:31:77:31:0,77,948 -20_10037292_10066351 14724 . T . . END=14726 GT:DP:GQ:MIN_DP:PL 0/0:29:84:29:0,84,1260 -20_10037292_10066351 14727 . T . . END=14727 GT:DP:GQ:MIN_DP:PL 0/0:31:78:31:0,78,941 -20_10037292_10066351 14728 . T . . END=14730 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 14731 . A . . END=14731 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 -20_10037292_10066351 14732 . G . . END=14734 GT:DP:GQ:MIN_DP:PL 0/0:31:82:30:0,82,942 -20_10037292_10066351 14735 . G . . END=14735 GT:DP:GQ:MIN_DP:PL 0/0:30:75:30:0,75,893 -20_10037292_10066351 14736 . C . . END=14736 GT:DP:GQ:MIN_DP:PL 0/0:31:87:31:0,87,1305 -20_10037292_10066351 14737 . A . . END=14737 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf.idx b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf.idx deleted file mode 100644 index 51256de7d..000000000 Binary files a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf.idx and /dev/null differ diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/main.nf.test b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/main.nf.test deleted file mode 100644 index e0996fb68..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/jointgenotyping/tests/main.nf.test +++ /dev/null @@ -1,42 +0,0 @@ -nextflow_process { - - name "Test Process GATK_JOINTGENOTYPING" - script "../main.nf" - process "GATK_JOINTGENOTYPING" - - test("family_trio [vcf] [idx]") { - - when { - params { - outdir = "tests/results" - } - process { - """ - input[0] = [ - file("${projectDir}/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf"), - file("${projectDir}/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf"), - file("${projectDir}/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf") - ] - input[1] = [ - file("${projectDir}/modules/local/gatk/jointgenotyping/tests/inputs/reads_father.bam.g.vcf.idx"), - file("${projectDir}/modules/local/gatk/jointgenotyping/tests/inputs/reads_mother.bam.g.vcf.idx"), - file("${projectDir}/modules/local/gatk/jointgenotyping/tests/inputs/reads_son.bam.g.vcf.idx") - ] - input[2] = file("${projectDir}/data/ref/intervals.bed") - input[3] = "family_trio" - input[4] = file("${projectDir}/data/ref/ref.fasta") - input[5] = file("${projectDir}/data/ref/ref.fasta.fai") - input[6] = file("${projectDir}/data/ref/ref.dict") - """ - } - } - - then { - assert process.success - assert path(process.out[0][0]).readLines().contains('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_father reads_mother reads_son') - assert path(process.out[0][0]).readLines().contains('20_10037292_10066351 3480 . C CT 1625.89 . AC=5;AF=0.833;AN=6;BaseQRankSum=0.220;DP=85;ExcessHet=0.0000;FS=2.476;MLEAC=5;MLEAF=0.833;MQ=60.00;MQRankSum=0.00;QD=21.68;ReadPosRankSum=-1.147e+00;SOR=0.487 GT:AD:DP:GQ:PL 0/1:15,16:31:99:367,0,375 1/1:0,18:18:54:517,54,0 1/1:0,26:26:78:756,78,0') - } - - } - -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/main.nf b/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/main.nf deleted file mode 100644 index 103a47631..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - conda "bioconda::samtools=1.20" - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/tests/main.nf.test b/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/tests/main.nf.test deleted file mode 100644 index 9d2d22c0f..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/tests/main.nf.test +++ /dev/null @@ -1,65 +0,0 @@ -nextflow_process { - - name "Test Process SAMTOOLS_INDEX" - script "../main.nf" - process "SAMTOOLS_INDEX" - - test("reads_son [bam]") { - - when { - params { - outdir = "tests/results" - } - process { - """ - input[0] = file("${projectDir}/data/bam/reads_son.bam") - """ - } - } - - then { - assert process.success - assert snapshot(process.out).match() - } - - } - test("reads_mother [bam]") { - - when { - params { - outdir = "tests/results" - } - process { - """ - input[0] = file("${projectDir}/data/bam/reads_mother.bam") - """ - } - } - - then { - assert process.success - assert snapshot(process.out).match() - } - - } - test("reads_father [bam]") { - - when { - params { - outdir = "tests/results" - } - process { - """ - input[0] = file("${projectDir}/data/bam/reads_father.bam") - """ - } - } - - then { - assert process.success - assert snapshot(process.out).match() - } - - } - -} diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/tests/main.nf.test.snap b/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/tests/main.nf.test.snap deleted file mode 100644 index 5f4b4bf66..000000000 --- a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/tests/main.nf.test.snap +++ /dev/null @@ -1,53 +0,0 @@ -{ - "reads_father [bam]": { - "content": [ - { - "0": [ - [ - "reads_father.bam:md5,57f3b977b0eee8278924e38894d02a57", - "reads_father.bam.bai:md5,49cb8454781a279a8b33f47209e76fe5" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.1", - "nextflow": "24.02.0" - }, - "timestamp": "2024-10-27T23:45:04.526628608" - }, - "reads_son [bam]": { - "content": [ - { - "0": [ - [ - "reads_son.bam:md5,af5956d9388ba017944bef276b71d809", - "reads_son.bam.bai:md5,a2ca7b84998218ee77eff14af8eb8ca2" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.1", - "nextflow": "24.02.0" - }, - "timestamp": "2024-10-27T23:26:47.056835774" - }, - "reads_mother [bam]": { - "content": [ - { - "0": [ - [ - "reads_mother.bam:md5,04b918c3707c24d8f3a7e88bb68e2d32", - "reads_mother.bam.bai:md5,1b17cbcc9392e7e787cc83a9081deb31" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.1", - "nextflow": "24.02.0" - }, - "timestamp": "2024-10-27T23:44:54.193439354" - } -} diff --git a/hello-nextflow/solutions/hello-nf-test/nf-test.config b/hello-nextflow/solutions/hello-nf-test/nf-test.config deleted file mode 100644 index feb82f052..000000000 --- a/hello-nextflow/solutions/hello-nf-test/nf-test.config +++ /dev/null @@ -1,8 +0,0 @@ -config { - - testsDir "." - workDir ".nf-test" - configFile "tests/nextflow.config" - profile "" - -} diff --git a/hello-nextflow/solutions/hello-nf-test/tests/main.nf.test b/hello-nextflow/solutions/hello-nf-test/tests/main.nf.test deleted file mode 100644 index 2f0e8956b..000000000 --- a/hello-nextflow/solutions/hello-nf-test/tests/main.nf.test +++ /dev/null @@ -1,21 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf" - script "main.nf" - - test("Should run without failures") { - - when { - params { - // outdir = "tests/results" - } - } - - - then { - assert workflow.success - } - - } - -} diff --git a/hello-nextflow/solutions/hello-nf-test/tests/nextflow.config b/hello-nextflow/solutions/hello-nf-test/tests/nextflow.config deleted file mode 100644 index 2514fbd50..000000000 --- a/hello-nextflow/solutions/hello-nf-test/tests/nextflow.config +++ /dev/null @@ -1,27 +0,0 @@ -/* -======================================================================================== - Nextflow config file for running tests -======================================================================================== -*/ - -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = "${projectDir}/data/sample_bams.txt" - - - // Output directory - params.outdir = "results_genomics" - - // Accessory files - reference = "${projectDir}/data/ref/ref.fasta" - reference_index = "${projectDir}/data/ref/ref.fasta.fai" - reference_dict = "${projectDir}/data/ref/ref.dict" - intervals = "${projectDir}/data/ref/intervals.bed" - - // Base name for final output file - cohort_name = "family_trio" -} diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-1.nf b/hello-nextflow/solutions/hello-operators/hello-operators-1.nf deleted file mode 100644 index a21486b1d..000000000 --- a/hello-nextflow/solutions/hello-operators/hello-operators-1.nf +++ /dev/null @@ -1,90 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input (file of input files, one per line) -params.reads_bam = "${projectDir}/data/sample_bams.txt" - -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) -} diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-2.nf b/hello-nextflow/solutions/hello-operators/hello-operators-2.nf deleted file mode 100644 index 5ed7c738e..000000000 --- a/hello-nextflow/solutions/hello-operators/hello-operators-2.nf +++ /dev/null @@ -1,133 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input (file of input files, one per line) -params.reads_bam = "${projectDir}/data/sample_bams.txt" - -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -// Base name for final output file -params.cohort_name = "family_trio" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} - -/* - * Combine GVCFs into GenomicsDB datastore - */ -process GATK_GENOMICSDB { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - - output: - path "${cohort_name}_gdb" - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - """ -} - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) - - // Collect variant calling outputs across samples - all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect() - all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect() - - // Combine GVCFs into a GenomicsDB datastore - GATK_GENOMICSDB( - all_gvcfs_ch, - all_idxs_ch, - intervals_file, - params.cohort_name - ) -} diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-3.nf b/hello-nextflow/solutions/hello-operators/hello-operators-3.nf deleted file mode 100644 index 1d7439107..000000000 --- a/hello-nextflow/solutions/hello-operators/hello-operators-3.nf +++ /dev/null @@ -1,146 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ - -// Primary input (file of input files, one per line) -params.reads_bam = "${projectDir}/data/sample_bams.txt" - -// Accessory files -params.reference = "${projectDir}/data/ref/ref.fasta" -params.reference_index = "${projectDir}/data/ref/ref.fasta.fai" -params.reference_dict = "${projectDir}/data/ref/ref.dict" -params.intervals = "${projectDir}/data/ref/intervals.bed" - -// Base name for final output file -params.cohort_name = "family_trio" - -/* - * Generate BAM index file - */ -process SAMTOOLS_INDEX { - - container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464' - - publishDir params.outdir, mode: 'symlink' - - input: - path input_bam - - output: - tuple path(input_bam), path("${input_bam}.bai") - - script: - """ - samtools index '$input_bam' - """ -} - -/* - * Call variants with GATK HaplotypeCaller - */ -process GATK_HAPLOTYPECALLER { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - tuple path(input_bam), path(input_bam_index) - path ref_fasta - path ref_index - path ref_dict - path interval_list - - output: - path "${input_bam}.g.vcf" , emit: vcf - path "${input_bam}.g.vcf.idx" , emit: idx - - script: - """ - gatk HaplotypeCaller \ - -R ${ref_fasta} \ - -I ${input_bam} \ - -O ${input_bam}.g.vcf \ - -L ${interval_list} \ - -ERC GVCF - """ -} - -/* - * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls - */ -process GATK_JOINTGENOTYPING { - - container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867" - - publishDir params.outdir, mode: 'symlink' - - input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict - - output: - path "${cohort_name}.joint.vcf" - path "${cohort_name}.joint.vcf.idx" - - script: - def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ') - """ - gatk GenomicsDBImport \ - ${gvcfs_line} \ - -L ${interval_list} \ - --genomicsdb-workspace-path ${cohort_name}_gdb - - gatk GenotypeGVCFs \ - -R ${ref_fasta} \ - -V gendb://${cohort_name}_gdb \ - -L ${interval_list} \ - -O ${cohort_name}.joint.vcf - """ -} - -workflow { - - // Create input channel from a text file listing input file paths - reads_ch = Channel.fromPath(params.reads_bam).splitText() - - // Load the file paths for the accessory files (reference and intervals) - ref_file = file(params.reference) - ref_index_file = file(params.reference_index) - ref_dict_file = file(params.reference_dict) - intervals_file = file(params.intervals) - - // Create index file for input BAM file - SAMTOOLS_INDEX(reads_ch) - - // Call variants from the indexed BAM file - GATK_HAPLOTYPECALLER( - SAMTOOLS_INDEX.out, - ref_file, - ref_index_file, - ref_dict_file, - intervals_file - ) - - // Collect variant calling outputs across samples - all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect() - all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect() - - // Combine GVCFs into a GenomicsDB data store and apply joint genotyping - GATK_JOINTGENOTYPING( - all_gvcfs_ch, - all_idxs_ch, - intervals_file, - params.cohort_name, - ref_file, - ref_index_file, - ref_dict_file - ) -} diff --git a/hello-nextflow/solutions/hello-world/hello-world-1.nf b/hello-nextflow/solutions/hello-world/hello-world-1.nf deleted file mode 100644 index a67f1016c..000000000 --- a/hello-nextflow/solutions/hello-world/hello-world-1.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -process sayHello { - - output: - stdout - - script: - """ - echo 'Hello World!' - """ -} - -workflow { - sayHello() -} diff --git a/hello-nextflow/solutions/hello-world/hello-world-2.nf b/hello-nextflow/solutions/hello-world/hello-world-2.nf deleted file mode 100644 index 53ee46f85..000000000 --- a/hello-nextflow/solutions/hello-world/hello-world-2.nf +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - output: - stdout - - script: - """ - echo 'Hello World!' - """ -} - -workflow { - - // emit a greeting - sayHello() -} diff --git a/hello-nextflow/solutions/hello-world/hello-world-4.nf b/hello-nextflow/solutions/hello-world/hello-world-4.nf deleted file mode 100644 index 026a593a8..000000000 --- a/hello-nextflow/solutions/hello-world/hello-world-4.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - publishDir 'results', mode: 'copy' - - output: - path 'output.txt' - - script: - """ - echo 'Hello World!' > output.txt - """ -} - -workflow { - - // emit a greeting - sayHello() -} diff --git a/hello-nextflow/solutions/hello-world/hello-world-7.nf b/hello-nextflow/solutions/hello-world/hello-world-7.nf deleted file mode 100644 index 401dc4ff9..000000000 --- a/hello-nextflow/solutions/hello-world/hello-world-7.nf +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ -params.greeting = "Bonjour le monde!" - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - publishDir 'results', mode: 'copy' - - input: - val greeting - - output: - path "output.txt" - - script: - """ - echo '$greeting' > "output.txt" - """ -} - -/* - * Use a text replace utility to convert the greeting to uppercase - */ -process convertToUpper { - input: - path input_file - - output: - path "UPPER-${input_file}" - - script: - """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file} - """ -} - -workflow { - - // create a channel for inputs - greeting_ch = Channel.of(params.greeting) - - // emit a greeting - sayHello(greeting_ch) - - // convert the greeting to uppercase - convertToUpper(sayHello.out) -} diff --git a/hello-nextflow/solutions/hello-world/hello-world-8.nf b/hello-nextflow/solutions/hello-world/hello-world-8.nf deleted file mode 100644 index 5b7eba63c..000000000 --- a/hello-nextflow/solutions/hello-world/hello-world-8.nf +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env nextflow - -/* - * Pipeline parameters - */ -params.greeting = "Bonjour le monde!" - -/* - * Use echo to print 'Hello World!' to standard out - */ -process sayHello { - - publishDir 'results', mode: 'copy' - - input: - val greeting - - output: - path "${greeting}-output.txt" - - script: - """ - echo '$greeting' > '$greeting-output.txt' - """ -} - -/* - * Use a text replace utility to convert the greeting to uppercase - */ -process convertToUpper { - input: - path input_file - - output: - path "UPPER-${input_file}" - - script: - """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file} - """ -} - -workflow { - - // create a channel for inputs - greeting_ch = Channel.of('Hello', 'Bonjour', 'Holà') - - // emit a greeting - sayHello(greeting_ch) - - // convert the greeting to uppercase - convertToUpper(sayHello.out) -} diff --git a/hello-nextflow/test-params.json b/hello-nextflow/test-params.json new file mode 100644 index 000000000..715feeffa --- /dev/null +++ b/hello-nextflow/test-params.json @@ -0,0 +1,5 @@ +{ + "greet": "greetings.csv", + "batch": "Trio", + "character": "turkey" +} diff --git a/mkdocs.yml b/mkdocs.yml index 6e981c7ce..75f47b6a9 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -11,16 +11,18 @@ nav: - envsetup/02_local.md - Hello Nextflow: - hello_nextflow/index.md - - hello_nextflow/01_orientation.md - - hello_nextflow/02_hello_world.md - - hello_nextflow/03_hello_containers.md - - hello_nextflow/04_hello_genomics.md - - hello_nextflow/05_hello_operators.md + - hello_nextflow/00_orientation.md + - hello_nextflow/01_hello_world.md + - hello_nextflow/02_hello_channels.md + - hello_nextflow/03_hello_workflow.md + - hello_nextflow/04_hello_modules.md + - hello_nextflow/05_hello_containers.md - hello_nextflow/06_hello_config.md - - hello_nextflow/07_hello_modules.md - - hello_nextflow/08_hello_nf-test.md - - hello_nextflow/09_hello_nf-core.md - - hello_nextflow/10_hello_seqera.md + - Nextflow for Genomics: + - nf4_science/genomics/index.md + - nf4_science/genomics/00_orientation.md + - nf4_science/genomics/01_per_sample_variant_calling.md + - nf4_science/genomics/02_joint_calling.md - Fundamentals Training: - basic_training/index.md - basic_training/orientation.md @@ -48,28 +50,6 @@ nav: - advanced/configuration.md - advanced/summary.md - advanced/support.md - - Configure nf-core: - - nf_customize/index.md - - nf_customize/01_orientation.md - - nf_customize/02_nf-core.md - - nf_customize/03_execution.md - - nf_customize/04_config.md - - nf_customize/05_tools.md - - Develop nf-core: - - nf_develop/index.md - - nf_develop/1_01_orientation.md - - nf_develop/1_02_create.md - - nf_develop/1_03_pipeline.md - - nf_develop/1_04_parameters.md - - Troubleshooting: - - troubleshoot/index.md - - troubleshoot/01_orientation.md - - troubleshoot/01_exercise.md - - troubleshoot/02_exercise.md - - troubleshoot/03_exercise.md - - troubleshoot/04_exercise.md - - troubleshoot/05_exercise.md - - troubleshoot/06_exercise.md theme: name: material @@ -129,7 +109,7 @@ extra: We use cookies to recognize your repeated visits and preferences, as well as to measure the effectiveness of our documentation and whether users find what they're searching for. With your consent, you're helping us to - make our documentation better. + make our training materials better. # Overridden in docs/assets/overrides/partials/social.html # Still needs to be set to something here so that the partial is used social: @@ -169,26 +149,21 @@ plugins: - enumerate-headings: restart_increment_after: - envsetup/01_setup.md - - hello_nextflow/01_orientation.md + - hello_nextflow/00_orientation.md + - nf4_science/genomics/00_orientation.md - basic_training/orientation.md - advanced/orientation.md - - nf_customize/01_orientation.md - - nf_develop/1_01_orientation.md - - troubleshoot/01_orientation.md exclude: - index.md - help.md - envsetup/index.md + - hello_nextflow/*.md + - nf4_science/genomics/*.md - basic_training/index.md + - basic_training/orientation.md - advanced/index.md - - hello_nextflow/index.md - - nf_customize/index.md - - nf_develop/index.md - - troubleshoot/index.md - - hands_on/index.md - - hands_on/solutions/*md - - hello_nextflow/*.md + - advanced/orientation.md - i18n: docs_structure: suffix fallback_to_default: true @@ -197,15 +172,15 @@ plugins: default: true locale: en name: English - - build: true + - build: false default: false locale: pt name: Português - - build: true + - build: false default: false locale: es name: Español - - build: true + - build: false default: false locale: fr name: Français diff --git a/hello-nextflow/data/bam/reads_father.bam b/nf4-science/genomics/data/bam/reads_father.bam similarity index 100% rename from hello-nextflow/data/bam/reads_father.bam rename to nf4-science/genomics/data/bam/reads_father.bam diff --git a/hello-nextflow/data/bam/reads_mother.bam b/nf4-science/genomics/data/bam/reads_mother.bam similarity index 100% rename from hello-nextflow/data/bam/reads_mother.bam rename to nf4-science/genomics/data/bam/reads_mother.bam diff --git a/hello-nextflow/data/bam/reads_son.bam b/nf4-science/genomics/data/bam/reads_son.bam similarity index 100% rename from hello-nextflow/data/bam/reads_son.bam rename to nf4-science/genomics/data/bam/reads_son.bam diff --git a/hello-nextflow/data/ref/intervals.bed b/nf4-science/genomics/data/ref/intervals.bed similarity index 100% rename from hello-nextflow/data/ref/intervals.bed rename to nf4-science/genomics/data/ref/intervals.bed diff --git a/hello-nextflow/data/ref/ref.dict b/nf4-science/genomics/data/ref/ref.dict similarity index 100% rename from hello-nextflow/data/ref/ref.dict rename to nf4-science/genomics/data/ref/ref.dict diff --git a/hello-nextflow/data/ref/ref.fasta b/nf4-science/genomics/data/ref/ref.fasta similarity index 100% rename from hello-nextflow/data/ref/ref.fasta rename to nf4-science/genomics/data/ref/ref.fasta diff --git a/hello-nextflow/data/ref/ref.fasta.fai b/nf4-science/genomics/data/ref/ref.fasta.fai similarity index 100% rename from hello-nextflow/data/ref/ref.fasta.fai rename to nf4-science/genomics/data/ref/ref.fasta.fai diff --git a/nf4-science/genomics/data/sample_bams.txt b/nf4-science/genomics/data/sample_bams.txt new file mode 100644 index 000000000..75ec2db60 --- /dev/null +++ b/nf4-science/genomics/data/sample_bams.txt @@ -0,0 +1,3 @@ +/workspace/gitpod/nf4-science/genomics/data/bam/reads_mother.bam +/workspace/gitpod/nf4-science/genomics/data/bam/reads_father.bam +/workspace/gitpod/nf4-science/genomics/data/bam/reads_son.bam diff --git a/nf4-science/genomics/data/samplesheet.csv b/nf4-science/genomics/data/samplesheet.csv new file mode 100644 index 000000000..2e17b27e6 --- /dev/null +++ b/nf4-science/genomics/data/samplesheet.csv @@ -0,0 +1,4 @@ +id,reads_bam +NA12878,/workspace/gitpod/nf4-science/genomics/data/bam/reads_mother.bam +NA12877,/workspace/gitpod/nf4-science/genomics/data/bam/reads_father.bam +NA12882,/workspace/gitpod/nf4-science/genomics/data/bam/reads_son.bam diff --git a/hello-nextflow/hello-genomics.nf b/nf4-science/genomics/genomics-1.nf similarity index 100% rename from hello-nextflow/hello-genomics.nf rename to nf4-science/genomics/genomics-1.nf diff --git a/hello-nextflow/hello-operators.nf b/nf4-science/genomics/genomics-2.nf similarity index 100% rename from hello-nextflow/hello-operators.nf rename to nf4-science/genomics/genomics-2.nf diff --git a/hands-on/bin/gghist.R b/other/hands-on/bin/gghist.R similarity index 100% rename from hands-on/bin/gghist.R rename to other/hands-on/bin/gghist.R diff --git a/hands-on/data/blacklist.bed b/other/hands-on/data/blacklist.bed similarity index 100% rename from hands-on/data/blacklist.bed rename to other/hands-on/data/blacklist.bed diff --git a/hands-on/data/genome.fa b/other/hands-on/data/genome.fa similarity index 100% rename from hands-on/data/genome.fa rename to other/hands-on/data/genome.fa diff --git a/hands-on/data/known_variants.vcf.gz b/other/hands-on/data/known_variants.vcf.gz similarity index 100% rename from hands-on/data/known_variants.vcf.gz rename to other/hands-on/data/known_variants.vcf.gz diff --git a/hands-on/data/reads/ENCSR000COQ1_1.fastq.gz b/other/hands-on/data/reads/ENCSR000COQ1_1.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COQ1_1.fastq.gz rename to other/hands-on/data/reads/ENCSR000COQ1_1.fastq.gz diff --git a/hands-on/data/reads/ENCSR000COQ1_2.fastq.gz b/other/hands-on/data/reads/ENCSR000COQ1_2.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COQ1_2.fastq.gz rename to other/hands-on/data/reads/ENCSR000COQ1_2.fastq.gz diff --git a/hands-on/data/reads/ENCSR000COQ2_1.fastq.gz b/other/hands-on/data/reads/ENCSR000COQ2_1.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COQ2_1.fastq.gz rename to other/hands-on/data/reads/ENCSR000COQ2_1.fastq.gz diff --git a/hands-on/data/reads/ENCSR000COQ2_2.fastq.gz b/other/hands-on/data/reads/ENCSR000COQ2_2.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COQ2_2.fastq.gz rename to other/hands-on/data/reads/ENCSR000COQ2_2.fastq.gz diff --git a/hands-on/data/reads/ENCSR000COR1_1.fastq.gz b/other/hands-on/data/reads/ENCSR000COR1_1.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COR1_1.fastq.gz rename to other/hands-on/data/reads/ENCSR000COR1_1.fastq.gz diff --git a/hands-on/data/reads/ENCSR000COR1_2.fastq.gz b/other/hands-on/data/reads/ENCSR000COR1_2.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COR1_2.fastq.gz rename to other/hands-on/data/reads/ENCSR000COR1_2.fastq.gz diff --git a/hands-on/data/reads/ENCSR000COR2_1.fastq.gz b/other/hands-on/data/reads/ENCSR000COR2_1.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COR2_1.fastq.gz rename to other/hands-on/data/reads/ENCSR000COR2_1.fastq.gz diff --git a/hands-on/data/reads/ENCSR000COR2_2.fastq.gz b/other/hands-on/data/reads/ENCSR000COR2_2.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000COR2_2.fastq.gz rename to other/hands-on/data/reads/ENCSR000COR2_2.fastq.gz diff --git a/hands-on/data/reads/ENCSR000CPO1_1.fastq.gz b/other/hands-on/data/reads/ENCSR000CPO1_1.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000CPO1_1.fastq.gz rename to other/hands-on/data/reads/ENCSR000CPO1_1.fastq.gz diff --git a/hands-on/data/reads/ENCSR000CPO1_2.fastq.gz b/other/hands-on/data/reads/ENCSR000CPO1_2.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000CPO1_2.fastq.gz rename to other/hands-on/data/reads/ENCSR000CPO1_2.fastq.gz diff --git a/hands-on/data/reads/ENCSR000CPO2_1.fastq.gz b/other/hands-on/data/reads/ENCSR000CPO2_1.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000CPO2_1.fastq.gz rename to other/hands-on/data/reads/ENCSR000CPO2_1.fastq.gz diff --git a/hands-on/data/reads/ENCSR000CPO2_2.fastq.gz b/other/hands-on/data/reads/ENCSR000CPO2_2.fastq.gz similarity index 100% rename from hands-on/data/reads/ENCSR000CPO2_2.fastq.gz rename to other/hands-on/data/reads/ENCSR000CPO2_2.fastq.gz diff --git a/hands-on/final_main.nf b/other/hands-on/final_main.nf similarity index 100% rename from hands-on/final_main.nf rename to other/hands-on/final_main.nf diff --git a/hands-on/nextflow.config b/other/hands-on/nextflow.config similarity index 100% rename from hands-on/nextflow.config rename to other/hands-on/nextflow.config diff --git a/nf-customize/data/gut_1.fastq.gz b/other/nf-customize/data/gut_1.fastq.gz similarity index 100% rename from nf-customize/data/gut_1.fastq.gz rename to other/nf-customize/data/gut_1.fastq.gz diff --git a/nf-customize/data/gut_2.fastq.gz b/other/nf-customize/data/gut_2.fastq.gz similarity index 100% rename from nf-customize/data/gut_2.fastq.gz rename to other/nf-customize/data/gut_2.fastq.gz diff --git a/nf-customize/data/liver_1.fastq.gz b/other/nf-customize/data/liver_1.fastq.gz similarity index 100% rename from nf-customize/data/liver_1.fastq.gz rename to other/nf-customize/data/liver_1.fastq.gz diff --git a/nf-customize/data/liver_2.fastq.gz 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b/other/troubleshoot/exercise3/nextflow.config similarity index 100% rename from troubleshoot/exercise3/nextflow.config rename to other/troubleshoot/exercise3/nextflow.config diff --git a/troubleshoot/exercise4/hello-gatk.nf b/other/troubleshoot/exercise4/hello-gatk.nf similarity index 100% rename from troubleshoot/exercise4/hello-gatk.nf rename to other/troubleshoot/exercise4/hello-gatk.nf diff --git a/troubleshoot/exercise4/nextflow.config b/other/troubleshoot/exercise4/nextflow.config similarity index 100% rename from troubleshoot/exercise4/nextflow.config rename to other/troubleshoot/exercise4/nextflow.config diff --git a/troubleshoot/exercise5/hello-gatk.nf b/other/troubleshoot/exercise5/hello-gatk.nf similarity index 100% rename from troubleshoot/exercise5/hello-gatk.nf rename to other/troubleshoot/exercise5/hello-gatk.nf diff --git a/troubleshoot/exercise5/nextflow.config b/other/troubleshoot/exercise5/nextflow.config similarity index 100% rename from troubleshoot/exercise5/nextflow.config rename to other/troubleshoot/exercise5/nextflow.config diff --git a/troubleshoot/exercise6/hello-gatk.nf b/other/troubleshoot/exercise6/hello-gatk.nf similarity index 100% rename from troubleshoot/exercise6/hello-gatk.nf rename to other/troubleshoot/exercise6/hello-gatk.nf diff --git a/troubleshoot/exercise6/nextflow.config b/other/troubleshoot/exercise6/nextflow.config similarity index 100% rename from troubleshoot/exercise6/nextflow.config rename to other/troubleshoot/exercise6/nextflow.config diff --git a/troubleshoot/hello-gatk.nf b/other/troubleshoot/hello-gatk.nf similarity index 100% rename from troubleshoot/hello-gatk.nf rename to other/troubleshoot/hello-gatk.nf diff --git a/troubleshoot/nextflow.config b/other/troubleshoot/nextflow.config similarity index 100% rename from troubleshoot/nextflow.config rename to other/troubleshoot/nextflow.config