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IMPUTE2

IMPUTE2

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.

Topic

Population genetics

Details

  • Operation: Phasing; imputation
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Linux; Mac OS X; Microsoft Windows; Solaris
  • License: GNU GPL 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: Gonalo R. Abecasis goncalo _at_ umich.edu | Jonathan Marchini marchini _at_ stats.ox.ac.uk | Matthew Stephens mstephens _at_ uchicago.edu
  • Collection: -

Publications

Howie B, Marchini J, Stephens M "Genotype imputation with thousands of genomes." G3 (Bethesda). 2011 Nov;1(6):457-70. https://doi.org/10.1534/g3.111.001198
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. https://doi.org/10.1038/ng.2354
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. https://doi.org/10.1038/ng2088
PMID: 17572673

Marchini J, Howie B "Genotype imputation for genome-wide association studies." Nat Rev Genet. 2010 Jul;11(7):499-511. https://doi.org/10.1038/nrg2796
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. https://doi.org/10.1371/journal.pgen.1000529
PMID: 19543373
PMCID: PMC2689936

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