From 870c523fb0985f1c81b1b11b888f019d6cc24488 Mon Sep 17 00:00:00 2001 From: LindoNkambule Date: Wed, 14 Feb 2024 12:30:16 -0500 Subject: [PATCH] minor syntax fix --- gwaspy/phasing/shapeit5_phase.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gwaspy/phasing/shapeit5_phase.py b/gwaspy/phasing/shapeit5_phase.py index 7bfac5b..dc8c5c0 100644 --- a/gwaspy/phasing/shapeit5_phase.py +++ b/gwaspy/phasing/shapeit5_phase.py @@ -45,7 +45,7 @@ def annotate_vcf( ) j.command(f""" - bcftools +fill-tags {vcf['vcf']} -Ou -- -t AN,AC -o {j.annotated_vcf['vcf']} + bcftools +fill-tags {vcf['vcf']} -Ou -o {j.annotated_vcf['vcf']} -- -t AN,AC bcftools index {j.annotated_vcf['vcf']} --output {j.annotated_vcf['index']} --threads {ncpu} """)