IMPUTE 4

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

Citation:

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 

Changelog:

21 July (v1.0) : First release

Usage:

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.

Help:

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

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=OXSTATGEN

IMPUTE 4 was written by Jonathan Marchini.