1000 Genomes Project SNPs

Question

[goodcow]

I want a file that has all the SNPs discovered by the 1000 genomes project, with their location and major/minor allele genotype and frequency. I need this in order to determine the haplotype of my sequences.

So far, I've looked at 1000 genomes project's Data Slicer and the UCSC Genome Browser, but I can't figure out how to get such a file. Could someone with experience with this please help me? Thanks!

[Kevin Blighe]

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

Answer 1

[Philipp Bayer]

The data-page of the 1000 Genomes project has two links to the NCBI and the EBI, these two seem to be the latest VCF files for all chromosomes:

• ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/
• ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/

You can then use wget to download all files from there:

wget -r --reject="index.html*" ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/

[goodcow]

So it seems like I would have to download the .vcf file for each chromosome? I'm wondering if there is a file that just has the consensus SNPs.

[Philipp Bayer]

In that case, maybe this older thread can help you: Identifying Snps Contributed By 1000Genomes Project