Pooled-heterozigosity (SECTION2)

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?

hp vcf pooled_heterozygosity

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written 4.7 years ago by reza

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