From 5d0b36658cc7921e785bc1a79b12081c0da7a5e4 Mon Sep 17 00:00:00 2001 From: Alistair Ward Date: Fri, 8 Nov 2024 13:33:35 -0700 Subject: [PATCH] 1. Changed comp het annotation from 1 to Pass --- generate_comphet_tsv.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generate_comphet_tsv.py b/generate_comphet_tsv.py index bfd6dcc..a15fac2 100644 --- 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