1000G Interim Phase I Haplotypes (2010-11 data freeze, 2011-06 haplotypes)
Original haplotypes (generated at the Baylor College of Medicine, by Fuli Yu and Yi Wang) are available
1000 Genomes Project FTP site.
This release includes haplotypes for a total of 1,094 individuals (breakdown pedigree file). All populations were analyzed together and at the same sites,
making cross population analysis simpler. Since this reference panel is relatively large, we recommend you use
minimac for imputation.
This set of phase haplotypes includes singletons (for completeness, although you probably won't be able to impute them very well!).
Note that ~200,000 SNPs changed their IDs from rsIDs to chr$chr:$position naming scheme because either the original rsIDs used can map to multiple positions in the genome; or their genomic position maps to multiple rs-IDs.
If you download before 2011-Aug-14, you may consider downloading again. As SNP names change, all files are affected except the haplotype files.