Population Level Allele Frequencies For The 1000 Genomes 20101123 Release

Question

[Tugrul]

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

[lh3]

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

[Laura]

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

Answer 1

[Jorge Amigo]

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.