Entering edit mode
2.5 years ago
reza
▴
300
Following the question I asked before and unfortunately did not receive any help, I have another question that I hope will benefit from your help.
For major and minor allele count I must use AD and DP in FORMAT section in VCF file? For example in the following conditions (one SNP for two sample) and while AF=0.136 (in INFO section of VCF file)
GT:AD:DP:GQ:PL 0/1:1,2:3:36:73,0,36 0/1:11,13:24:99:371,0,424
nMAJ = 12 (Ref as mojor allele because AF is less than 0.5) and nMIN = 15 (ALT as minor allele)?
Is this method correct to calculate nMAJ and nMIN?
