Bcftools isec GT aware

[Rashesh7]

Hello,

Is there a way to run bcftools isec with taking genotypes into consideration? I want to compare multiple VCF files and check even in the same variant call, how many have a shift from heterozygous to homozygous.

I am running "bcftools isec -p Unique -n-1 -c none $FILE1 $FILE2 $FILE3 ...." currently. But it just checks for the exact Alt allele. I know vcf-compare has an option for comparing genotypes "--cmp-genotypes ". Is there something similar that I can use?

Many Thanks, Rashesh

[pd3]

I wonder if the GTisec or GTsubset plugins would help. I did not write these so can't really tell.