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Haplotype caller AF - How to obtain the real AFSpectrum.
Hi GATK team,
I just figure out recently that the vcf I produced with HC was producing theoretical allele frequencies. But I would like to have an allele frequency per population (I can always sub-devide my vcf if needed) and I was wondering if there is any way to get this done via GATK or if you knew a way to obtain this information,
Thanks a lot in advance,