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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
from the
1000 Genomes Project FTP site. The sub-population and continental group information for the 1,092 individuals can be found
at (
phase1_integrated_calls.20101123.ALL.panel. A breakdown by continents is pasted below:
- AFR 246
- AMR 181
- ASN 286
- EUR 379
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.
If you have any questions email Christian Fuchsberger, or Yun Li.
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