How To Retrieve Allele Frequency For A Large Data ?

Question

[prajwalnj]

Hello,

I have a list of variants (37,000) for which I would like to retrieve its minor allele frequency mainly from the European population.

There are many known variants ( from dbSNP 135) and novel snps. I tried using UCSC table browser but it just tells me the 'submitter' and not the population from where it comes from. Is there a way to do this for so many variants ?

Thank you.

[zx8754]

Getting allele frequencies from 1000 genomes

Answer 1

[Sean Davis]

Besides 1000genomes, if your data are exomes (37k variants sounds like an exome), you might try the Exome Sequencing Project:

http://evs.gs.washington.edu/EVS/

Answer 2

[Emily]

Have you tried the Ensembl API? You can use Perl to look up each of your SNPs in the database and retrieve the allele frequencies from the 1000 genomes populations. http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PopulationGenotype.html