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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?