1,000 Genomes haplotypes -- Phase I integrated variant set release in NCBI build 37 (hg19) coordinates

   --These files are based on a sequence data freeze from 21 May 2011; the phased haplotypes were released Oct 2011.

   --The haplotypes include an integrated set of SNPs, insertion/deletion polymorphisms, and structural variants. The haplotypes were inferred from sequence data by BEAGLE (Brian and Sharon Browning, University of Washington) and MaCH/Thunder (Yun Li, University of North Carolina and Goncalo Abecasis, University of Michigan).

   --The original haplotypes can be downloaded as VCF ("variant call format") files from the 1000 Genomes FTP site.

Haplotype, legend, sample, and genetic map files Download packages (warning: large files) This download contains reference data for 1,092 individuals from Africa, Asia, Europe, and the Americas. We provide one worldwide haplotype file for each chromosome since we recommend using all available reference haplotypes with IMPUTE2, regardless of the ancestry of your study data. For background information on this approach, see here. If you really want to use just a subset of the haplotypes, you can manually parse the haplotype files with a utility like the linux 'cut' command. The sample file that comes in the download package contains the information needed to subset the files. When using these combined panels, you should set the -Ne argument of IMPUTE2 to 20000, as explained here. You should use IMPUTE version 2.2 or later to ensure proper handling of these reference panels.  [ALL]