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IMPUTE is a program for estimating ("imputing") unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. There are currently three different versions of the IMPUTE software available for download: version 0.5 implements the methodology described in Marchini et al. (2007); version 1 is essentially the same as version 0.5, with a couple of added features; and version 2 implements a major extension that was introduced in Howie et al. (2009)

Official Homepage
Users Manual
These links explains the command-line argument that can be used to control IMPUTE

Option Type Description
Required arguments The program will no run if these ar not supplied.
Input file options A list of possible ionput files, with formatting requirements.
Output file options  Naming conventions and options for controlling format of output files.
Basic options Options for controlling how the program processes input data.
Stand allgnment options Options for allgning allele coding across data files.
Filtering options Options for controlling the filters that get applied to input data.
MCMC options Options for controlling the MCMC algorithm.
Expert option Options to be used by experts only.

Other References
  1. J. Marchini, B. Howie, S. Myers, G. McVean and P. Donnelly (2007) A new multipoint method for genome-wide association studies via imputation of genotypes. Nature Genetics 39: 906-913 [Free Access PDF] [Supplementary Material] [News and Views Article]
  2. B. N. Howie, P. Donnelly and J. Marchini (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genetics 5(6): e1000529 [Open Access Article]
  3. J. Marchini and B. Howie (2010) Genotype imputation for genome-wide association studies. Nature Reviews Genetics 11: 499-511 [Restricted Access PDF] [Supplementary Material]
License Agreement and Citation Format
License Agreement

Citation Format 
If you use IMPUTE2 in a published manuscript, please cite Howie et al. (2009, PLoS Genetics).
How to Access the Program 
Servers Versions Paths Parallelization Methods
Aurora 2.1.0 /apps/Impute/2.1.0  
Using the Program
Additional Notes

Last Updated - 4th Oct 2011
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