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Population Level Allele Frequencies For The 1000 Genomes 20101123 Release

Hi,

A couple of months ago, Laura mentioned that they did not have yet the population level allele frequencies for the latest 1000 genomes data release, i.e., the 20101123 release.

http://biostar.stackexchange.com/questions/9550/why-so-many-missing-genotypes-in-1000-genomes-data

I checked the directory (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20101123) to see if they already published the AF information, however, it does not seem they did.

AF info only exists separately for the calls from each institute.

Does anyone know if they publish population level AF information somewhere else?

Thanks

genome allele
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updated by Jorge Amigo Jorge Amigo • written by Tugrul • Tugrul

This not available right now, so far as I know.

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written by lh3 lh3

nope we still only have global allele frequencies, You can use the genotype files to get AC/AN based estimates but these may be inaccurate

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written by Laura Laura

1 answer

on that folder there's a file called ALL.wgs.phase1.projectConsensus.snps.sites.vcf.gz which should contain all the variant sites discovered by 1000 genomes, and where the allele frequencies should be reported as "AF" codes. it won't be split by population though (you would have to do that manually yourself by processing the genotypes), but referring to the entire world population.

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written by Jorge Amigo Jorge Amigo

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