fixing allelic imbalance filtering bcftools command

PMBio · Oct 21, 2024 · 8e45654 · 8e45654
1 parent 87d5f41
commit 8e45654
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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: