IMPUTE5

Description

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 optim-ized 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 Trans-form (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 haplo-types as conditioning states within the IMPUTE model.

Environment Modules

Run module spider IMPUTE5 to find out what environment modules are available for this application.

System Variables

HPC_IMPUTE5_DIR - installation directory
HPC_IMPUTE5_BIN - executable directory

Additional Information

Three commands are made available for this module:

imp5Chunker
imp5Converter
impute5

Job Script Examples

See the IMPUTE5_Job_Scripts page for IMPUTE5 Job script examples.

Citation

If you publish research that uses IMPUTE5 you have to cite it as follows:

Rubinacci S, Delaneau O, Marchini J (2020) Genotype imputation using the Positional Burrows Wheeler Trans- form. PLOS Genetics 16(11): e1009049