Table 5. Performance and running time for GeneImp and BEAGLE imputation of chromosome 22 (16 target samples).
| Method | Mean- | Time in hra | Allocated CPUsb |
|---|---|---|---|
| GeneImp; single-window | 0.907 | 1.5 | 16 parallel processes (doMC R package) |
| GeneImp; five-window-average | 0.922 | 9.0 | 16 parallel processes (doMC R package) |
| BEAGLE | 0.939 | 135.6 | 32 parallel threads (nthreads option) |
a
We report the elapsed time between start and finish of the experiment. This was recorded using the time unix command for BEAGLE and the proc.time() R function for GeneImp. The server was solely used for this job during this time.
b
Experiments performed on a server with 4× Intel Xeon E7-4870 processors, with 2.40 GHz and 10 cores (20 threads) each and 256 GB RAM.