This is a test version of Biostars. For the public version, visit https://www.biostars.org.
snps/indels with individual genotypes from 1000 genomes ftp site

Sorry if this might be a trivial question!

I read a lot about this until I got lost. I need to download wgs VCF file from the 1000 genomes ftp site. I need the snps (snvs and indels), most importantly, I need to have the individual genotypes of all the persons involved.

so for example, this file :

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz

which was referenced many times on biostars, does not contain individual genotypes. I need something similar to what those files contain. Is there one global file containing snps/indels for wgs data including genotypes of the various samples ?

thanks!

1000 genomes ftp genotypes vcf
• 4,061 views • link
updated by hk5 • hk5 • written by lait lait

1 answer

You can download the entire data per chromosome (chr1-22 & chrX) —including individual genotypes for both indels and SNPs— using this code:

prefix="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr" ;

suffix=".phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" ;

for chr in {1..22} X; do
    wget $prefix$chr$suffix $prefix$chr$suffix.tbi ;
done

From: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format

Kevin

• 1 views • link
written by Kevin Blighe Kevin Blighe

thanks a lot !!.....

• 0 views • link
written by lait lait

I can't get the files, it says the host is not resolvable. I tried also from the NCBI website, none of the pages can be opened. Is there another way to download the human vcf files directly from the terminal?

• 1 views • link
written by marongiu.luigi marongiu.luigi

I can connect - I did it just now 10 seconds ago. To where are you downloading the data?

• 1 views • link
written by Kevin Blighe Kevin Blighe

The direct links are: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr4.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr5.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr7.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
et cetera

...and, the tab-index files:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
et cetera

• 1 views • link
updated by GenoMax GenoMax • written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this