Where to download official reference and alternative alleles from 1000 Genomes?

Question

[Mr Locuace]

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 !

Answer 1

[chrchang523]

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 .

[GenoMax]

OP Wants to get the reference genome.

Answer 2

[GenoMax]

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

[Mr Locuace]

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

[GenoMax]

See Heng Li's blog post here.

[Mr Locuace]

Thanks very much @genomax !