It looks like the GATK forums site is down this whole week so I am unable to get an answer to a somewhat basic question.
I have generated several VCF files of individual haploid samples using GATK 18.104.22.168 and the variants have their allele frequencies as 1. I would like to calculate their empirical allele frequencies for subsequent plotting of their site frequency spectrum. How do I go about this?
Thanks in advance!