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Calculating allele frequencies in pooled samples

wschackwschack JGI - Walnut Creek CAMember

I am resequencing a sample extracted from an aliquot taken from an evolved population, and am looking for a tool that will 1) call variants, both snps and indels, that are at low allele frequency within the sample, and 2) report an estimate of the allele frequency of the variant allele within that sample. Can Haplotype Caller do this? I see that the polidy tool has been added, but does it also return estimated allele freq of the variant allele within each individual sample?


  • valentinvalentin Cambridge, MAMember, Dev ✭✭

    As you pointed out, you can turn up the -ploidy argument for pooled samples to increase the allele frequency resolution; to calculate AF in 5% increments you would need to set the ploidy to 20. The math in HaplotypeCaller assumes that is dealing with a single individual with that many genome copies; so it won't try to guess the ploidy at a site nor try to report smaller AF fractions.

    If you run each sample individually, the info annotation MLEAF would contain a ML point estimate of the allele frequency for that sample (I think the frequency of the ref alleles is omitted but can be calculated as 1 - sum(MLEAF)). That should match what you would get if you count the number of occurrences of each allele in the GT annotation for the sample and divide by the ploidy. So if you prefer to run HaplotypeCaller on severals samples you can process the GTs to obtain individual sample AF estimates.

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