Question: How to extract total allele frequency from gnomAD annotation
gravatar for yasminsoareslima
8 days ago by
yasminsoareslima10 wrote:

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?


gnmoad af allelefrequency • 81 views
ADD COMMENTlink modified 8 days ago by manuel.belmadani460 • written 8 days ago by yasminsoareslima10


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 REPLYlink modified 8 days ago • written 8 days ago by RamRS20k
gravatar for manuel.belmadani
8 days ago by
manuel.belmadani460 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 COMMENTlink written 8 days ago by manuel.belmadani460

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 REPLYlink written 8 days ago by yasminsoareslima10

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 REPLYlink modified 7 days ago • written 7 days ago by manuel.belmadani460
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