The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Minor Allele Frequency filter in GATK
I'm working on a resequencing dataset , which contains 60 individuals from 5 different populations. I used HaplotypeCaller to conduct variants calling, and got all individuals in one big dataset after applying hard filter, then I would like to know if in GATK, can I apply minor allele frequency filter to one specific population considering I have 5 different populations in one file?