Fix Allelic Imbalance Filtering Logic for bcftools v1.16+

[HolEv]

Fixing issue #134

What

This update addresses an issue with the bcftools allelic imbalance filtering command introduced in versions later than v1.16. Specifically, we want to exclude (write) variants only where all heterozygous calls have an allele balance (AB) < 0.15, but keep the variant if any heterozygous call has an AB > 0.15.

The previous bcftools allelic imbalance filtering command

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}}

only had the intended behavior until bcftools v1.16. With newer versions, bcftools filtering logic seem sot have changed from an any to all evaluation.
This results in all heterozygous variants being written to the variants to exclude file for versions > v1.16, even if a call meets the AB criterion.

The fixed bcftools command (suggested by @rdey-inistro)

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}} 

has the intended version for either bcftools version (<=v1.16 & >v1.16).

Testing

The expected behavior of the new command was verified on the example vcf file using bcftools versions 1.12, 1.16, 1.18, 1.20.