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!
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.