Filtering for Homozygous Variants
I am trying to use an or statement to select for homozygous opposite genotypes between two samples in select variants. I have tried some variations but never been able to get what I am looking for in the outcome. Can you please advise what is going wrong here.
Options in use are:
-env -noTrim --selectTypeToExclude INDEL -select 'vc.getGenotype("SampleA").isHomVar() || vc.getGenotype("SampleA").isHomRef()' --selectexpressions "AF==0.500" --restrictAllelesTo BIALLELIC
If I can select for either HomVar or HomRef for that sample, then the AF should take care of ensuring the second sample is homozygous for the opposite genotype with the AF.