1000G Phase I Integrated Release Version 3 Haplotypes
(2010-11 data freeze, 2012-03-14 haplotypes)
The release contains haplotypes on 1092 samples (#haplotypes = 2184) for total ~39.7M bi-allelic polymorphic markers.
Among the ~39.7M million markers, ~1.4M are short indels and large deletions, the rest SNPs.
Latest version of MaCH/MaCH-Admix and
minimac can handle vcf format.
Original data available
1000 Genomes Project FTP site. The sub-population and continental group information for the 1,092 individuals can be found
phase1_integrated_calls.20101123.ALL.panel. A breakdown by continents is pasted below:
This set of phase haplotypes includes singletons (for completeness, although you probably won't be able to impute them very well!).
Monomorphic sites are removed.
- AFR 246
- AMR 181
- ASN 286
- EUR 379
If you have any questions email Christian Fuchsberger, or Yun Li.