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 | Â | Â | 23,042 | 23,042 | 0.901 | |
MaCH | Â | Â | 21,998 | 21,998 | 0.944 | |
fastPHASE | Â | Â | 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 |