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
Detail
Operation: Phasing;imputation
Software interface: Command-line user interface
Language: Perl
License: GNU General Public License v3
Cost: -
Version name: 2.3.2
Credit: The National Human Genome Research Institute (NHGRI), United Kingdom Medical Research Council, The National Institutes of Health (NIH)
Input: -
Output: -
Contact: Gonçalo R. Abecasis goncalo@umich.edu | Jonathan Marchini marchini@stats.ox.ac.uk | Matthew Stephens mstephens@uchicago.edu
Collection: -
Maturity: Mature
Publications
- Fast and accurate genotype imputation in genome-wide association studies through pre-phasing.
- Howie B, et al. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. 2012; 44:955-9. doi: 10.1038/ng.2354
- https://doi.org/10.1038/ng.2354
- PMID: 22820512
- PMC: PMC3696580
- A new multipoint method for genome-wide association studies by imputation of genotypes.
- Marchini J, et al. A new multipoint method for genome-wide association studies by imputation of genotypes. A new multipoint method for genome-wide association studies by imputation of genotypes. 2007; 39:906-13. doi: 10.1038/ng2088
- https://doi.org/10.1038/ng2088
- PMID: 17572673
- PMC: -
- Genotype imputation for genome-wide association studies.
- Marchini J and Howie B. Genotype imputation for genome-wide association studies. Genotype imputation for genome-wide association studies. 2010; 11:499-511. doi: 10.1038/nrg2796
- https://doi.org/10.1038/nrg2796
- PMID: 20517342
- PMC: -
- A flexible and accurate genotype imputation method for the next generation of genome-wide association studies.
- Howie BN, et al. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. 2009; 5:e1000529. doi: 10.1371/journal.pgen.1000529
- https://doi.org/10.1371/journal.pgen.1000529
- PMID: 19543373
- PMC: PMC2689936
- Genotype imputation with thousands of genomes.
- Howie B, et al. Genotype imputation with thousands of genomes. Genotype imputation with thousands of genomes. 2011; 1:457-70. doi: 10.1534/g3.111.001198
- https://doi.org/10.1534/g3.111.001198
- PMID: 22384356
- PMC: PMC3276165
Download and documentation
Source: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download
Documentation: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#getting_started
Home page: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
Data: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference
Links: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#examples
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