Question: Filtering on MAF using the GATK?
0
gravatar for jtwalker
2.4 years ago by
jtwalker20
jtwalker20 wrote:

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!

ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 2.4 years ago by jtwalker20

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

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum124k

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

ADD REPLYlink written 2.4 years ago by jtwalker20
1

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Pierre Lindenbaum124k

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

ADD REPLYlink written 2.4 years ago by jtwalker20
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