RT Journal Article
SR Electronic
T1 Genotype imputation using the Positional Burrows Wheeler Transform
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 797944
DO 10.1101/797944
A1 Simone Rubinacci
A1 Olivier Delaneau
A1 Jonathan Marchini
YR 2019
UL http://biorxiv.org/content/early/2019/10/09/797944.abstract
AB Genotype imputation is the process of predicting unobserved genotypes in a sample of individuals using a reference panel of haplotypes. Increasing reference panel size poses ever increasing computational challenges for imputation methods. Here we present IMPUTE5, a genotype imputation method that can scale to reference panels with millions of samples. It achieves fast and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT), which are used as conditioning states within the IMPUTE model. IMPUTE5 is 20x faster than MINIMAC4 and 3x faster than BEAGLE5, when using the HRC reference panel, and uses less memory than both these methods. IMPUTE5 scales sub-linearly with reference panel size. Keeping the number of imputed markers constant, a 100 fold increase in reference panel size requires less than twice the computation time.