IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2  method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE 5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as conditioning states within the IMPUTE model.

IMPUTE5 is up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.1



If you use IMPUTE 5 in your research, please cite the following publication:

S. Rubinacci, O. Delaneau, J. Marchini (2019) Genotype imputation using the Positional Burrows Wheeler Transform PLoS Genetics [Journal] [bioRxiv]

Latest version:

13 January 2021 : Version 1.1.4

Software registration and license:

IMPUTE 5 is freely available for academic use only. To see rules for non-academic use see the LICENCE file (also included with each software download).

The software and LICENCE can be found here


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