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Old 08-28-2014, 07:41 AM   #1
huma Asif
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Location: Japan

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Default continent-specific variants

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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Old 08-28-2014, 07:52 AM   #2
cariboudoug
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Default

The populations included in the 1000 genomes are described here:
http://www.1000genomes.org/category/...ons/population

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

Quote:
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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