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IMPUTE2 is a tool for genotype imputation and haplotype phasing. The IMPUTE2 algorithm uses 'pre-phasing' wherein it makes initial statistical estimates of the haplotypes. In the next step, it imputes missing genotypes given the estimated haplotypes. This approach yields reduced computing time.


Population genetics


  • Operation: Phasing; imputation
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Linux; Mac OS X; Microsoft Windows; Solaris
  • License: GNU General Public License v3
  • Cost: -
  • Version name: 2.3.2
  • Maturity: Mature
  • Credit: The National Human Genome Research Institute (NHGRI), United Kingdom Medical Research Council, The National Institutes of Health (NIH)
  • Contact: Gonçalo R. Abecasis goncalo _at_ | Jonathan Marchini marchini _at_ | Matthew Stephens mstephens _at_
  • Collection: -


Howie B, Marchini J, Stephens M "Genotype imputation with thousands of genomes." G3 (Bethesda). 2011 Nov;1(6):457-70.
PMID: 22384356
PMCID: PMC3276165

Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR "Fast and accurate genotype imputation in genome-wide association studies through pre-phasing." Nat Genet. 2012 Jul 22;44(8):955-9.
PMID: 22820512
PMCID: PMC3696580

Marchini J, Howie B, Myers S, McVean G, Donnelly P "A new multipoint method for genome-wide association studies by imputation of genotypes." Nat Genet. 2007 Jul;39(7):906-13. Epub 2007 Jun 17.
PMID: 17572673

Marchini J, Howie B "Genotype imputation for genome-wide association studies." Nat Rev Genet. 2010 Jul;11(7):499-511.
PMID: 20517342

Howie BN, Donnelly P, Marchini J "A flexible and accurate genotype imputation method for the next generation of genome-wide association studies." PLoS Genet. 2009 Jun;5(6):e1000529.
PMID: 19543373
PMCID: PMC2689936

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