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Minor Allele Frequency filter in GATK

Hi all,
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?

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Answers

  • @Sheila
    Thanks for your kind answer, I would like to have a try.

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