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Estimating allele frequency in pooled data (AD / DP fields)

Hi folks,

I am using GATK to call SNPs and indels on pooled population samples, with ~50 individuals per pool (barcode). I intend on using the AD (allele depth) fields for the reference and alternate alleles to calculate allele frequency in the population; however, it appears that the AD field is not quality filtered- only the DP field is, which lacks alt vs ref counts. Am I understanding this correctly? Is there a way to output the # of reads for both the reference and alternate alleles, post-filtering?

Thanks,
Heather Machado
Stanford University

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