Does VarScan2 find somatic mutations that arose in loci where norm was heterozygous? As far as I can tell, it classifies somatic changes as "Somatic" (but that seems to only include homozygous normal) and "loss of heterozygosity", where normal was hetereozygous, and tumor is homozygous". What happens if normal was heterozygous, and tumor has 3 alleles (one novel)? I don't seem to be able to find such sites in VarScan output.
Thank you,
Elena
Thank you,
Elena
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