Question: Population Level Allele Frequencies For The 1000 Genomes 20101123 Release
4
gravatar for Tugrul
8.1 years ago by
Tugrul40
Tugrul40 wrote:

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 • 2.1k views
ADD COMMENTlink modified 7.9 years ago by Jorge Amigo11k • written 8.1 years ago by Tugrul40

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

ADD REPLYlink written 8.1 years ago by lh331k

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

ADD REPLYlink written 8.0 years ago by Laura1.7k
1
gravatar for Jorge Amigo
8.1 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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.

ADD COMMENTlink written 8.1 years ago by Jorge Amigo11k
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