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.
Environment Variables¶
- HPC_IMPUTE5_DIR - installation directory
- HPC_IMPUTE5_BIN - executable directory
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 Transform. PLoS genetics, 16(11), e1009049. https://doi.org/10.1371/journal.pgen.1009049
Categories¶
biology, math