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Calculating allele frequencies in pooled samples
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?