Is there a quick way to get allele read depth for all possible alleles say from bam or mpileup?
10 101023 . A G,T 220 . DP=35;VDB=0.0407;AF1=1;AC1=2;DP4=0,0,14,11;MQ=43;FQ=-99 GT:PL:GQ 1/1:253,72,0,247,52,244:99
2 89159986 . T A,C 193 . DP=52;VDB=6.418245e-02;AF1=1;AC1=2;DP4=0,0,29,23;MQ=23;FQ=-181 GT:PL:DP:SP:GQ 1/1:226,154,0,211,122,208:52:0:99
one possiblity is to parse the mpileup output?.