Impute5

Description:

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

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

Usage:

• module load impute5

• imp5Chunker_1.1.5_static  

• imp5Converter_1.1.5_static  

• impute5_1.1.5_static