1000 Genomes Vcf File

Question

[win]

hi all. i was wondering if someone could let point me the direction of the VCF file from 1000 genomes which has from all chromosomes for all samples?

thanks in advance.

Answer 1

[fatstrat389]

You can find the VCF files for phase 1 here: ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/

[win]

those are individual chromosome fies, i believe there is one file with data from all chromosomes but i cannot seem to find that.

[matted]

Try vcf-concat?

[Laura]

Or if you only need the sites you can use the wgs file ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz

If you want the genotypes a file which was the whole genome would be so big as to be unmanageable so we only provide files by chromosome

[win]

does this file have genotypes for the sites?

[Adam]

There haven't been any "whole genome" VCFs produced by the 1000 Genomes Project since the Pilot phase.