Table 2.
Run time and accuracy for phasing, and haploid imputation methods on the real dataset scenario
| 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 |
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
HD high-density, LD low-density