Question: Does 1000 genomes have a flat file with allele frequencies for each site anywhere?
0
gravatar for curious
6 weeks ago by
curious450
curious450 wrote:

I know how to download all the vcfs from query the info fields to get allele frequency:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

and I have been doing this. I am wondering if there is a flat file that exits anywhere that has the non-genotype VCF fields or just the allele frequency for each site for different populations. So you can get allele frequency without having to download those big vcfs.

This seem like it would be a handy thing to have so I wonder if I am just missing it.

1000 genomes • 379 views
ADD COMMENTlink modified 6 weeks ago by cmdcolin1.4k • written 6 weeks ago by curious450
1

ANNOVAR had compiled something like that, you could install it and pull the datafiles out.

ADD REPLYlink written 6 weeks ago by karl.stamm3.8k
0
gravatar for curious
6 weeks ago by
curious450
curious450 wrote:

Its here:

wget -O af.vcf.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
ADD COMMENTlink written 6 weeks ago by curious450
0
gravatar for cmdcolin
6 weeks ago by
cmdcolin1.4k
United States
cmdcolin1.4k wrote:

Might look at ALFA

Ref

https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/

Some flatfiles, run bigBedToBed to convert to bed

https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/

Read https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/ALFA.html

ADD COMMENTlink written 6 weeks ago by cmdcolin1.4k
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