1,000 Genomes Phase I haplotypes (interim release) -- NCBI Build 37

   --These files are based on a sequence data freeze from 23 Nov 2010; the phased haplotypes were released Jun 2011.

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

   --The original haplotypes can be downloaded from the 1000 Genomes FTP site.

Haplotype, legend, sample, and genetic map files

This download contains the latest reference dataset from the 1,000 Genomes Project, which includes 1,094 individuals from around the world. We provide a single, worldwide haplotype file for each chromosome since we have found that it is usually best to use all available reference haplotypes with IMPUTE2. For background information on this approach, see here.

If you have a good reason to use a subset of the haplotypes, there are two options:
  1. Download a continent-specific file from here.

  2. Use the sample file that comes with the download to manually parse the haplotype files, using a utility like the linux 'cut' command.
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