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Table 1 Run time and accuracy for diploid imputation, phasing, and haploid imputation methods in the default simulated data scenario

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

Phasing method Imputation method Computing time (s) Accuracy
HD phasing LD phasing Imputation Total
  IMPUTE2    42,796 42,796 0.861
Beagle v4.0    23,042 23,042 0.901
MaCH    21,998 21,998 0.944
fastPHASE    28,892 28,892 0.941
HAPI-UR IMPUTE2 117 14 149 280 0.964
HAPI-UR Minimac3 117 14 62 193 0.967
HAPI-UR Beagle v4.1 117 14 78 209 0.793
Eagle2 IMPUTE2 1361 207 148 1717 0.988
Eagle2 Minimac3 1361 207 55 1623 0.988
Eagle2 Beagle v4.1 1361 207 79 1647 0.794
SHAPEIT2 IMPUTE2 8495 1175 150 9820 0.979
SHAPEIT2 Minimac3 8495 1175 58 9728 0.977
SHAPEIT2 Beagle v4.1 8495 1175 77 9747 0.792
  1. The run time is given in seconds separately for phasing and imputation steps and as a total
  2. HD high-density, LD low-density