continent-specific variants

huma Asif

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Join Date: Oct 2010

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#1

continent-specific variants

08-28-2014, 06:41 AM

Dear All,
Can any body help me in how can i extract continent specific variants from 1000 genome All population variant set
e.g i have downloaded 1000G_phase1.snps.high_confidence.hg19.vcf from GATK resource bundle and from this file i want to extract variants specific to e.g east asian ancestry
Any help will be appreciated
Regards
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cariboudoug

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Join Date: Oct 2013

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#2

08-28-2014, 06:52 AM

The populations included in the 1000 genomes are described here:

1000genomes.org - 1000genomes Resources and Information.

http://www.1000genomes.org/category/frequently-asked-questions/population

1000genomes.org is your first and best source for all of the information you’re looking for. From general topics to more of what you would expect to find here, 1000genomes.org has it all. We hope you find what you are searching for!

In that VCF you're talking about I think the allele frequency ("AF") is split up for these super-populations:

These populations have been divided into 5 super populations

AFR, African
AMR, Ad Mixed American
ASN, East Asian
EUR, European
SAN, South Asian

If those groupings aren't too general and you were interested in East Asian unique alleles than you could look at each SNP and only take those where ASN_AF > 0 and all other super populations have frequencies equal to 0.

Cheers,
Gavin
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