Dear all, we call insertion/deletions on 30 exomes and then split our VarScan .vcf into one per sample. This leads to many lines showing multi-allelic variants. However, our final .vcf do not contain allelic frequencies (FREQ) for each of the alleles but only for one (the first one, I assume). Is this intended, and is there a workaround for it? Thanks you very much in advance for your help! Leonor