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Compare VCFs against background frequencies

Hi everyone,

I have a bunch of VCF files for many human individuals, and I would like to test for variant enrichment with respect to background levels. I have no clue on where to start, I would really appreciate some guidance on the kind of tools I can use or where I can find data for this (or by any means studies that use this approach).

Many thanks in advance.

population vcf genomes 1000 variants genetics
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updated by Ram Ram • written by miguellarrazlopezdenovales • miguellarrazlopezdenovales

I'm a little unsure from your description, but it sound like you want to look at population structure. If so, you could use divergence metrics such as Fst or Dxy (which can be inferred using packages like PopGenome), or tools like STRUCTURE.

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written by dthorbur dthorbur

It's not clear to me what you are asking for? Do you want to compare the allele frequencies of your samples against a data set of 'controls'?

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written by 4galaxy77 4galaxy77

Hi, the issue is that I do not have a control dataset for this sample, so I am trying to find variant allele frequencies to compare my variants for enrichment. Thanks!

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written by miguellarrazlopezdenovales • miguellarrazlopezdenovales

OK, I understand. You could try downloading some frequencies from e.g. gnomad.

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written by 4galaxy77 4galaxy77

1 answer

If you want a 'comparison set' of allele frequencies, then gnomAD and alfa are two options.

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written by 4galaxy77 4galaxy77

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