From 8e456549553c5e568dda7e54b4797f4e725b7aef Mon Sep 17 00:00:00 2001 From: Eva Holtkamp Date: Mon, 21 Oct 2024 10:20:15 +0200 Subject: [PATCH] fixing allelic imbalance filtering bcftools command --- pipelines/preprocessing/qc.snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/preprocessing/qc.snakefile b/pipelines/preprocessing/qc.snakefile index 2369de45..950b1b00 100644 --- a/pipelines/preprocessing/qc.snakefile +++ b/pipelines/preprocessing/qc.snakefile @@ -8,7 +8,7 @@ rule qc_allelic_imbalance: resources: mem_mb=lambda wildcards, attempt: 256 * attempt, shell: - f"""{load_bcftools} bcftools query --format '%CHROM\t%POS\t%REF\t%ALT\n' --exclude 'COUNT(GT="het")=0 || (GT="het" & ((TYPE="snp" & (FORMAT/AD[*:1] / FORMAT/AD[*:0]) > 0.15) | (TYPE="indel" & (FORMAT/AD[*:1] / FORMAT/AD[*:0]) > 0.20)))' {{input}} | gzip > {{output}}""" + f"""{load_bcftools} bcftools query --format '%CHROM\t%POS\t%REF\t%ALT\n' --exclude 'COUNT(GT="het")=0 || COUNT(GT="het" & ((TYPE="snp" & (FORMAT/AD[*:1] / FORMAT/AD[*:0]) > 0.15) | (TYPE="indel" & (FORMAT/AD[*:1] / FORMAT/AD[*:0]) > 0.20)))>0' {{input}} | gzip > {{output}}""" rule qc_varmiss: