Compare VCFs against background frequencies

Question

[miguellarrazlopezdenovales]

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.

[dthorbur]

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.

[4galaxy77]

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'?

[miguellarrazlopezdenovales]

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!

[4galaxy77]

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

[miguellarrazlopezdenovales]

On it! Thanks :)

Answer 1

[4galaxy77]

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