Filtering on MAF using the GATK?

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7.5 years ago

jtwalker ▴ 20

I am using the GATK to jointly genotype several hundred samples. After this step I would like to do all of my filtering using the GATK, and would like to filter on MAF. Does anyone know if this is possible, or will I have to use Plink to do so?

Thanks!

gatk GATK variant filtering SNP filtering • 2.8k views

ADD COMMENT • link updated 7.4 years ago by Biostar 20 • written 7.5 years ago by jtwalker ▴ 20

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is the MAF available in the VCF ? do you have any multi-allelic alleles in the VCF (= more than one MAF per line)

ADD REPLY • link 7.5 years ago by Pierre Lindenbaum 164k

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No. I was wondering if the GATK had a tool that could calculate MAF from the VCF.

ADD REPLY • link 7.5 years ago by jtwalker ▴ 20

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I think every time you're running a GATK tool modifying the genotypes, the AC/AN attributes are re-calculated.

ADD REPLY • link 7.5 years ago by Pierre Lindenbaum 164k

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That's good to know. I appreciate the answer! Thanks

ADD REPLY • link 7.5 years ago by jtwalker ▴ 20

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