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).

To go to the webpage for a particular version of the program, just click the corresponding link below. Or, click the Background link to read a short description of what each version of the program does.

Version 0.5
Version 1
Version 2
Registration and Updates
Contact Information

Registration and Updates (top)

To sign up for e-mail reminders about updates to all versions of IMPUTE, just fill out the registration form.

References (top)

[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]

Contact Information (top)

If you have any questions regarding the use of these programs, please send an e-mail to both of the following people:

Dr. Bryan Howie (
bhowie <at> uchicago <dot> edu).
Dr. Jonathan Marchini ( marchini <at> stats <dot> ox <dot> ac <dot> uk).

It is a good idea to include a copy of the screen output (which is printed to the "summary" output file) with your e-mail to help us identify any problems.