IMPUTE 2.3.2

IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009:

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] [Supplementary Material]

IMPUTE2 also includes features that were introduced in other publications, which you can find here.

Accessing the software

To load the module:

$ module load apps/impute2/2.3.2

An example command to include in your job script:

$ impute2 \
  -m <recombination_map> \
  -g <genotype_file> \
  -int <genomic_lower_bound> <genomic_upper_bound> \


Example: IMPUTE2 Job

An example can be found at ${BB_EXAMPLES}/IMPUTE2/ The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/IMPUTE2 ~/impute2-test
$ cd ~/impute2-test

Edit the script according to your needs, then do:

$ sbatch

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the website for more information on this application.


Last modified: 19 July 2017