How to calculate popmax values for gnomAD variants?

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3.2 years ago

Brady • 0

I'm trying to use the gnomAD data to build a noise filter. We want to filter variants from our .vcf's that have a popmax value greater than a certain threshold, but I'm having trouble figuring out how to calculate popmax.

We've already downloaded the gnomAD .vcf.bgz files (separated by chromosome). The tabix package was recommended to me as a way to easily handle and manipulate these large files. But I cannot figure out how to use tabix to accomplish this.

Does anyone know if it's possible to use tabix to infer popmax values for variants in a vcf?

vcf popmax tabix gnomAD • 1.2k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 3.2 years ago by Brady • 0

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Did you figure out how? I am also new to this and have no idea how to proceed with the files

ADD REPLY • link 2.5 years ago by stientist • 0

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Do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate instead. I've moved your post to a comment now.

ADD REPLY • link 2.5 years ago by Ram 44k

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