1000 Genomes Project SNPs
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8.6 years ago
goodcow ▴ 20

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!

SNP genome 1000-genomes • 4.9k views
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8.6 years ago

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/
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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.

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

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