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Filtering on MAF using the GATK?

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
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updated by Biostar Biostar • written by jtwalker • jtwalker

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by jtwalker • jtwalker

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by jtwalker • jtwalker

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