University of Michigan Center for Statistical 


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.

Download Data

  ALL phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz (4.4Gb)
AFR phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.AFR.vcf.gz.tgz (1.3Gb) AMR phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.AMR.vcf.gz.tgz (0.7Gb) ASN phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ASN.vcf.gz.tgz (0.7Gb) EUR phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.EUR.vcf.gz.tgz (1.1Gb)

Marker Allelic Information

These map files are provided so that one can get information for the two alleles of each marker, particularly for indels since MaCH output reserves only 5 characters for the two alleles in the marker name.

GIANT ALL reference panel (no monomorphic and singleton sites)

ALL GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz (3.9Gb)

X-Chromosome (requires minimac.8.5.12 or newer)
ALL GIANT.chrX.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz (0.3Gb)

METABOCHIP ALL population reference panel (no monomorphic and singleton sites)

ALL GIANT.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz (0.9Gb)

Pre-calibrated parameters for MaCH-Admix

For more information, see MaCH-Admix Tutorial: Pick A RunMode


University of Michigan | School of Public Health | Abecasis Lab