How to extract total allele frequency from gnomAD annotation

Question: How to extract total allele frequency from gnomAD annotation

8 days ago by

Hello people,

I am quite confused about to extract the information I want from the Genomad annotation database (downloaded .vcf ). I've download the .vcf from Genomad and annotated using SnPEff, which resulted in maaany informations, for instance, the allele frequencies from each population, from controls, non_cancer, topmed, etc.

However, what interests me is the total allele frequency, the same as it appears in the browser version. The only annotation I could see that approximates from this is the "AF_raw", but when I compared to the browser version, I saw it was not the same for some variants. Could anyone tell me which INFO could I extract from my vcf to obtain this information?

Thanks!

gnmoad af allelefrequency • 81 views

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modified 8 days ago by manuel.belmadani • 460 • written 8 days ago by yasminsoareslima • 10

GenomAD

Do you mean gnomAD? Please give us a couple of example loci where you see a difference between the browser and your VCF. For those loci, also paste the entire INFO values here so we can see what's going on.

ADD REPLY • link modified 8 days ago • written 8 days ago by RamRS ♦ 20k

8 days ago by

manuel.belmadani • 460

Canada

manuel.belmadani • 460 wrote:

In the gnomAD vcf, the allele frequency should be the "AF=XXXXXX", for example "AF=3.28019e-05" for rs1411594174. The AF_raw field for this variant is indeed slightly different.

There's also subsets and population specific frequencies, like "AF_eas_female".

ADD COMMENT • link written 8 days ago by manuel.belmadani • 460

yeah, but it seems I dont have the information "AF" in my vcf, that's why I'm wondering how it is being called or how it is annotated. Perhaps it comes with a different name, I don't know.

ADD REPLY • link written 8 days ago by yasminsoareslima • 10

I'm not sure then, seems like a SnpEff specific issue. Try looking up for examples where SnpEff was used with gnomAD data, or post the steps required (every command line and file obtained) to reproduce your problem. An example SNP/variant where you see the AF_raw field but not the AF_ALL one could be useful too (post the entire line with annotations).

Or you could also use annovar. I often annotated VCFs using Annovar and the annotation for gnomad AF was named gnomAD_genome_ALL (there's also exome ones, that's somewhat specific to the way the annovar database was built).

ADD REPLY • link modified 7 days ago • written 7 days ago by manuel.belmadani • 460

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