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

   --These files are based on a sequence data freeze from 23 Nov 2010; the phased haplotypes were released Jun 2011. For more details, see the README file.

   --The haplotypes were inferred from sequence data by the SNPTools software (Fuli Yu and Yi Wang, Baylor College of Medicine).

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

   --Updated 06 Feb 2012 to include chromosome X haplotypes and continent-group-level minor allele frequencies in legend files.

   --Updated 05 Mar 2012 to exclude monomorphic sites and fix a small problem in the chrX nonPAR genetic map file.

   --Updated 19 Apr 2012 to exclude monomorphic sites that were not removed in the previous update.

Haplotype, legend, sample, and genetic map files
Download packages (warning: large files)
This download contains reference data for 1,094 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 2.2.0 or later if you want to use the -filt_rules_l option with these reference panels.