A program for efficient genotype imputation

  • IMPUTE 4 implements the haploid imputation options included in IMPUTE 2, but is much faster and more memory efficient.
  • It was written to impute genotypes for the UK Biobank dataset that consists of genetic data on ~500,000 individuals


If you use IMPUTE 4 in your research, please cite the following publication:

Bycroft et al. (2017) Genome-wide genetic data on ~500,000 UK Biobank participants 


21 July (v1.0) : First release


A basic command to run imputation on the example files included with the package is

./impute4 \
-h example/ref.hap.gz \
-l example/ref.legend \
-m example/genetic_map_chr20_combined_b37.txt \
-g example/test.haps.gz \
-int 2000000 3000000 \
-no_maf_align \
-Ne 20000 \
-o_gz \
-o example/output

A full list of arguments and details of file formats are listed here.

Software registration and license:

IMPUTE 4 is freely available for academic use only. To see rules for non-academic use see the LICENCE file (also included with each software download). Please register for access to the software here.


Please join the OXSTATGEN mailing list and then post any questions there

IMPUTE 4 was written by Jonathan Marchini.