how to call somatic of homozygosity?
hi, does gatk support call somatic of homozygosity?
Lets assume, we have a diploid cell (which is not always the case for e.g. tumor cells which can have copy number variations). If variant A (e.g. a SNV) is homozygous, you expect to see 100% of the reads from your exome-seq or wgs (lets assume NGS doesnt produce errors) containing this variant. If this variant is heterozygous (so one chromosome has the variant A and the other has the wildtype , you expect to see 50% of the reads to contain A and 50% of the reads to contain B.
so is it ok for gatk to do this, thanks a lot