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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