1. Changed comp het annotation from 1 to Pass

iobio · Nov 8, 2024 · 5d0b366 · 5d0b366
1 parent ec6d86a
commit 5d0b366
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/generate_comphet_tsv.py b/generate_comphet_tsv.py
@@ -51,7 +51,7 @@ def parse_command_line():
 def process_vcf(bcftools, vcf, output_file):
 
   # Loop over all records in the vcf file
-  command = bcftools + ' query -f \'%CHROM\\t%POS\\t%END\\t%REF\\t%ALT\\t1\\n\' ' + str(vcf)
+  command = bcftools + ' query -f \'%CHROM\\t%POS\\t%END\\t%REF\\t%ALT\\tPass\\n\' ' + str(vcf)
   for record in os.popen(command).readlines():
 
     # Split the record on tabs