Suggestion: Increase the default heteroplasmy filter to 10%

[EddieLF]

In the default variant search criteria, the sample heteroplasmy is filtered to show variants with heteroplasmy values in the range defined by vafRange: [0.02, 1].

A more sensible default value for this is 0.1, or 10%, which is still rather low. This would align to gnomAD, and would filter out artefacts and unlikely candidate variants.

mitoreport/ui/src/shared/constants.js

Line 54 in 3699eb5

vafRange: [0.02, 1],

[tommyli]

Thanks for the suggestion. I'll ask the group and get back to you.

[bellmartin]

Hi Eddie,
We consulted the mito team before setting the default heteroplasmy at 0.02 .
Although you do get some artefacts coming through at this level, there are pathogenic variants that can have a heteroplasmy at 2-10% . Especially in blood samples as the person ages.

We have found having the maternal heteroplasmy levels next to the proband's very useful in identifying potentially uninteresting variants and highlighting de novo ( or increased in heteroplasmy levels) variants, especially at the low levels.

Of course it just comes down to what you are willing to report or chase up.