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TableĀ 2 Run time and accuracy for phasing, and haploid imputation methods on the real dataset scenario

From: Assessment of the performance of hidden Markov models for imputation in animal breeding

Phasing method Imputation method Computing time (h) Accuracy
HD phasing LD phasing Imputation Total
HAPI-UR IMPUTE2 11.53 43.09 5.63 60.25 0.997
HAPI-UR Minimac3 11.53 43.09 2.27 56.89 0.995
HAPI-UR Beagle v4.1 11.53 43.09 2.69 57.31 0.939
Eagle2 IMPUTE2 4.48 (8 cores) 2.37 (8 cores) 5.63 12.48 0.827
Eagle2 Minimac3 4.48 (8 cores) 2.37 (8 cores) 2.21 9.06 0.992
Eagle2 Beagle v4.1 4.48 (8 cores) 2.37 (8 cores) 4.19 11.04 0.925
  1. The run time is given in hours separately for phasing and imputation steps and as a total. For Eagle2, the program was run distributed across 8 compute cores. HAPI-UR was run on a single core
  2. HD high-density, LD low-density