Question: 1000 Genomes Project SNPs
2
gravatar for goodcow
5.4 years ago by
goodcow20
United States
goodcow20 wrote:

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 (http://www.1000genomes.org/data-slicer) and the UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/hgTables), but I can't figure out how to get such a file. Could someone with experience with this please help me? Thanks! 

snp 1000-genomes genome • 3.2k views
ADD COMMENTlink modified 5.4 years ago by Philipp Bayer6.5k • written 5.4 years ago by goodcow20

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

ADD REPLYlink written 19 months ago by Kevin Blighe50k
0
gravatar for Philipp Bayer
5.4 years ago by
Philipp Bayer6.5k
Australia/Perth/UWA
Philipp Bayer6.5k wrote:

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/

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Philipp Bayer6.5k

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.

ADD REPLYlink written 5.4 years ago by goodcow20

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

ADD REPLYlink written 5.4 years ago by Philipp Bayer6.5k
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