commit 02/11/2021 12:55:03

Gabaldonlab · Nov 2, 2021 · 90c59d4 · 90c59d4
1 parent dede55f
commit 90c59d4
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/perSVade.py b/scripts/perSVade.py
@@ -903,7 +903,7 @@
     outdir_varcall = "%s/smallVars_CNV_output"%opt.outdir
 
     # define the basic cmd
-    varcall_cmd = "%s -r %s --threads %i --outdir %s -sbam %s --caller %s --coverage %i --mitochondrial_chromosome %s --mitochondrial_code %i --gDNA_code %i --minAF_smallVars %s --window_freebayes_bp %i --log_file_all_cmds %s"%(varcall_cnv_pipeline, opt.ref, opt.threads, outdir_varcall, sorted_bam, opt.caller, opt.coverage, opt.mitochondrial_chromosome, opt.mitochondrial_code, opt.gDNA_code, opt.minAF_smallVars, opt.window_freebayes_bp, log_file_all_cmds)
+    varcall_cmd = "%s -r %s --threads %i --outdir %s -sbam %s --caller %s --coverage %i --mitochondrial_chromosome %s --mitochondrial_code %i --gDNA_code %i --minAF_smallVars %s --window_freebayes_bp %i --log_file_all_cmds %s"%(varcall_cnv_pipeline, opt.ref, opt.threads, outdir_varcall, sorted_bam, opt.caller, opt.coverage, opt.mitochondrial_chromosome, opt.mitochondrial_code, opt.gDNA_code, opt.minAF_smallVars, opt.window_freebayes_bp, fun.log_file_all_cmds)
 
     # add options
     if opt.replace is True: varcall_cmd += " --replace"