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!
1 answer
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/
•
written
by
Philipp Bayer
In that case, maybe this older thread can help you: Identifying Snps Contributed By 1000Genomes Project
Log in to answer this question.
-
How do I annotate 1000 genomes VCF with superpopulation minor allele frequency?
written by Isobel •
-
Extract Info from chromosome locations
written by BDK_compbio
-
downloading GTF file as gzip format from UCSC website
written by modarzi
-
esiRNA sequences in Drosophila
written by Habil
-
Is there a parent-child SNP genotyping data available somewhere?
written by sinorenjianyi •
-
How to find exact allele frequency for the SNP/indel variants ?
written by MAPK
-
microRNA transcription start site prediction
written by paulamic •
-
Mapping Refseq Ng_ Regions To Chromosome Position
written by nmb •
-
Hg19 Bed File Compatible With Gatk
written by kanwarjag
-
How To Select Only One Human Genome Build (Hg19) From The Encode Project'S Data
written by Eric Ho •
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format