Entering edit mode
7.3 years ago
Phismil
▴
20
Dear colleagues , I am running stack to analyze pool seq data. I am wondering how do we identify reference versus alternative alleles in the VCF out put file ? We usually assume that the alleles that are more abundant are ancestral (reference) and less abundant alleles are derived(alternative) alleles. How ever it is not always obvious in DP : AD field of the VCF files : eg., less reads supports reference alleles compared with alternative alleles. Many thanks in advance
