Question: little discrepancies gnomAD DB vs. website
1
gravatar for cocchi.e89
13 months ago by
cocchi.e8950
cocchi.e8950 wrote:

I found that the latest DB (downloadable here) have little discrepancies respect the website data displayed.

As example (exome data):

16-90162186-T-C DB allele frequency: 0.371754 vs website (https://gnomad.broadinstitute.org/variant/16-90162186-T-C) AF: 0.3775

12-133435716-T-G DB AF: 0.22511 vs website (https://gnomad.broadinstitute.org/variant/12-133435716-T-G) AF: 0.2241

and the same results for population and GENOMES data. Does anybody has got a clue?

Thanks a lot in advance for any help!

ADD COMMENTlink modified 13 months ago by tpoterba50 • written 13 months ago by cocchi.e8950

I think this is a known discrepancy. Maybe someone more familiar with gnomAD can explain exactly why this happens.

ADD REPLYlink written 13 months ago by RamRS27k

What do you mean by "DB"? The vcf files one can download?

Please notice that in gnomAD they divide the frequency in exomes and genomes. The data you are showing for "DB" looks like the exome data, where else the "website" data looks like the total (exome+genome) data.

fin swimmer

ADD REPLYlink written 13 months ago by finswimmer13k

Yes VCF files downloaded, I’m well aware of it, I’m speaking about both (in example of exomes data) but is the same for genomes.

ADD REPLYlink modified 13 months ago • written 13 months ago by cocchi.e8950
0
gravatar for tpoterba
13 months ago by
tpoterba50
tpoterba50 wrote:

Looking at your 16-90162186-T-C example, the AF in the VCF/HT is 0.37175. The allele frequency listed under "exomes" on the browser at your link is 0.3718. These match.

The 0.3775 number is the total AF -- a weighted average cross the genomes and exomes.

ADD COMMENTlink written 13 months ago by tpoterba50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1399 users visited in the last hour