Table 5.
Runtime (CPU time) in hours and as factors for imputation and phasing.
| Tools | Runtime in hours | Runtime as factors | ||
|---|---|---|---|---|
| Imputation | Phasing | Imputation | Phasing | |
| Beagle5.1 | 5.81 | 3.50 | 2.18 | 1 |
| Beagle4.1 | 31.65 | 11.85 | ||
| Eagle2.4.1* | 4.47 | 1.28 | ||
| Eagle2.4.1 | 4.68 | 1.33 | ||
| IMPUTE2 | 34.57 | 12.95 | ||
| IMPUTE4 | 32.73 | 12.26 | ||
| minimac3 | 57.29 | 21.46 | ||
| minimac4 | 48.69 | 18.24 | ||
| PBWT | 2.67 | 1 | ||
| SHAPEIT2 | 14.07 | 4.02 | ||
| SHAPEIT2* | 24.20 | 6.91 | ||
For the factors, the fastest tool within imputation and phasing programs was chosen as factor one. For this table, the gain of speed due to parallelization is disregarded, since it is highly dependent on the local machines and chunking. Intel Xeon E5-2680 CPUs were used for phasing and imputation. Phasing tools marked with an asterix indicate the use of a reference panel for phasing.