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!
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
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:
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/
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.
In that case, maybe this older thread can help you: Identifying Snps Contributed By 1000Genomes Project
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