University of Michigan Center for Statistical 


1000G PhaseI v3 Shapeit2 Reference
(2010-11 data freeze, 2013-09 haplotypes)

The release contains haplotypes on 1092 samples (#haplotypes = 2184) for 36.8 million SNPs, 1.4 million indels, and 14 thousand SVs.

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
If you have any questions email Christian Fuchsberger, or Yun Li.

ALL reference panel - no monomorphic sites

ALL.SHAPEIT2_integrated_phase1_v3.20101123.snps_indels_svs.genotypes.all.noMono.tgz (4.6Gb)

ALL reference panel - no monomorphic and no singleton sites (recommended)

ALL.SHAPEIT2_integrated_phase1_v3.20101123.snps_indels_svs.genotypes.all.noSingleton.tgz (4.1Gb)

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)


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