1,000 Genomes haplotypes -- Pilot release in NCBI build 36 (hg18) coordinates

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

   --The haplotypes were inferred from sequence data by three different methods (Beagle at Broad Institute; MaCH at University of Michigan; MARGARITA at Sanger Institute) and then merged by IMPUTE2.

   --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)
These downloads contain reference data for 60 CEU individuals, 62 CHB+JPT individuals, and 59 YRI individuals.

After these reference panels were created, it was discovered that the CHB+JPT panel is poorly phased, which causes a substantial decrease in imputation accuracy from this panel. We have therefore decided not to provide the CHB+JPT haplotypes for download. You can download improved haplotypes for all panels here.