Hello,
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.
Thank you,
Amanda