How to download VCF of 1000 genome project with population frequencies?

Question

[bioinforesearchquestions]

Hi folks,

I would like to grab the population frequencies for a list of SNPs from 1000 genome project (https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/ ).

Currently, I am searching one snp at a time and downloading as a VCF. Is there a way for me to search my list and get the entire population data for my SNPs?

Do we have any commandline tool to handle this requirement?

Answer 1

[sf21]

I would suggest downloading the sites VCF from here, http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ and using bcftools to subset it to SNPs of interest using the -R or -T flag.

Link to the sites file: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi

[elisheva]

Are these files contain the SNPs of the populations in the entire genome? I would like to compare allele frequencies of the North European population vs the African population, is it possible?

Answer 2

[chrchang523]

The three boldfaced links at https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 provide one solution. With that dataset downloaded, plink2 can report allele frequencies for any predefined population, as well as any population you define yourself. (You can also export VCF files from it, and subsetting is frequently >10x faster than bcftools.)

Answer 3

[finswimmer]

Hello bioinforesearchquestions ,

if you are able to code use ensembl's REST-API, especially the variation endpoint. There also an endpoint for query multiple IDs at once.

fin swimmer