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 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.

Haplotype, legend, sample, and genetic map 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 have found that it is best to use all available reference haplotypes with IMPUTE2, regardless of the ancestry of the samples you want to impute. 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 by using the sample file that comes in the download package along with a utility like the linux 'cut' command.

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