Question: Where to download official reference and alternative alleles from 1000 Genomes?
0
gravatar for Mr Locuace
2.4 years ago by
Mr Locuace100
Chile
Mr Locuace100 wrote:

Hello, using Plink 1.9, I merged to cohorts of individuals that were genotyped at the same ~1700000 SNPs. I would like to check if the SNPs are in the same strand. For this, I need a file with the official reference and alternative alleles. Since most of my SNPs intersect with SNPs of 1000 Genomes, I would like to download reference/alternative alleles for these SNPs from 1000 Genomes. However, I am not able to find where can I download this info. Any suggestion would be welcomed !

ADD COMMENTlink modified 2.4 years ago by chrchang5237.1k • written 2.4 years ago by Mr Locuace100
2
gravatar for chrchang523
2.4 years ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

See ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ for 1000 Genomes phase 3 VCFs, and ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ for phase 1.

Phase 1 plink-formatted files with reference alleles in the 6th .bim column can be downloaded from https://www.cog-genomics.org/plink/1.9/resources#1kg .

ADD COMMENTlink written 2.4 years ago by chrchang5237.1k

OP Wants to get the reference genome.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax85k
0
gravatar for genomax
2.4 years ago by
genomax85k
United States
genomax85k wrote:

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference

ADD COMMENTlink written 2.4 years ago by genomax85k

Thanks very much @genomax. Which file would that be?

ADD REPLYlink written 2.4 years ago by Mr Locuace100

See Heng Li's blog post here.

ADD REPLYlink written 2.4 years ago by genomax85k

Thanks very much @genomax !

ADD REPLYlink written 2.4 years ago by Mr Locuace100
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