Introducing field-programmable gate arrays in genotype phasing and imputation

SUMMARY: 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 allows the user to choose a more resource-intensive parameter setting in exchange for computation time to further improve phasing and imputation quality. AVAILABILITY AND IMPLEMENTATION: EagleImp and its FPGA extension are freely available at https://github.com/ikmb/eagleimp and https://github.com/ikmb/eagleimp-fpga.