Introducing Field-Programmable Gate Arrays in Genotype Phasing and Imputation

Abstract

Abstract We recently developed EagleImp, a free software that combines genotype phasing and imputation in a single tool. By introducing algorithmic and technical improvements we accelerated the classical two-step approach using Eagle2 and PBWT. Here, we demonstrate how to use Field-Programmable Gate Arrays (FPGAs) to accelerate EagleImp even further by a factor of up to 93% without loss of phasing and imputation quality. Due to the speed advantage over a not accelerated processor-based implementation, the FPGA-extension of EagleImp offers the user the ability to choose a more resource-intensive parameter setting in exchange for computation time to further improve phasing and imputation quality. EagleImp and its FPGA-extension are freely availabe at https://github.com/ikmb/eagleimp and https://github.com/ikmb/eagleimp-fpga.