Question: How To Retrieve Allele Frequency For A Large Data ?
1
gravatar for prajwalnj
6.5 years ago by
prajwalnj10
USA
prajwalnj10 wrote:

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.

allele • 1.7k views
ADD COMMENTlink modified 6.5 years ago by Emily_Ensembl19k • written 6.5 years ago by prajwalnj10
2

Getting allele frequencies from 1000 genomes

ADD REPLYlink written 6.5 years ago by zx87548.2k
1
gravatar for Sean Davis
6.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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/

ADD COMMENTlink written 6.5 years ago by Sean Davis25k
0
gravatar for Emily_Ensembl
6.5 years ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

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

ADD COMMENTlink written 6.5 years ago by Emily_Ensembl19k
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