Where/how to get population specific AF for a set of SNPs
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3.0 years ago
heso ▴ 40


I'm trying to retrieve population specific (EUR) allele frequencies for a few hundred SNPs I got from the GWAS Catalog. Somehow, I can't find any of those SNPs in the 1000 genomes vcf file ( ftp://ftp.ensembl.org/pub/release-91/variation/vcf/homo_sapiens/1000GENOMES-phase_3.vcf.gz), but searching for them via the Ensembl webpage works well (and gives data that they have also been called in the 1000 genomes phase 3).

According to the FAQ the data in the GWAS Catalog is currently mapped to genome assembly GRCh38.p12 and dbSNP Build 150, hence should match the 1000GENOMES-phase_3.vcf (stated above). I also tried using BioMart, but could only retrieve the Global AF :(

So, is there any way to get the EUR AF through BioMart or any other way/source than the 1000 genomes?

I'll paste just a few SNPs here that I want the EUR_AF for (e.g. in case somebody wants to try out a code): rs61839660, rs1265564, rs2304256, rs941576, rs539514, rs478222, rs924043 etc.

Thanks to all responders :)

SNP allele frequency • 1.3k views
Entering edit mode
3.0 years ago

You can try gnomAD : http://gnomad.broadinstitute.org/


edit : @totj70 already proposed gnomAD ;)

Entering edit mode
3.0 years ago
totj70 • 0

1000genomes data is available (as far as I am aware) in both GRCh37 and GRCh38 - I would check that you have downloaded the right assembly VCF as that may be your problem.

If you do have the GRCh37 VCF for 1000Genomes, it may be easier to convert your SNPs from 38 -> 37 (instead of downloading the GRCh38 VCF), UCSC has a good tool to do this: https://genome.ucsc.edu/cgi-bin/hgLiftOver

I also use gnomAD in addition to 1000Genomes as it has way more European samples (although some of these individuals come from disease datasets, it is good for a general population allele frequency - just something to be aware of) http://gnomad.broadinstitute.org/about you can download the VCF, or you can search the gnomAD website manually.

Hope this helps! Good luck


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