Table 4.
–indep-pairwise runtimes (sec)
| Parameters | Dataset | Machine | PLINK 1.07 | PLINK 1.90 | Ratio |
|---|---|---|---|---|---|
| 50 5 0.5 | synth1 | Mac-2 | 701.3 | 0.63 | 1.1 k |
| Mac-12 | 569.4 | 0.55 | 1.0 k | ||
| Linux32-8 | 572.7 | 0.95 | 600 | ||
| Linux64-512 | 462 | 0.60 | 770 | ||
| Win32-2 | 1163.9 | 3.2 | 360 | ||
| Win64-2 | 1091.9 | 1.0 | 1.1 k | ||
| 700 70 0.7 | synth2 | Mac-2 | ∼120 k | 31.9 | 3.8 k |
| Mac-12 | 63.0 k | 20.6 | 3.06 k | ||
| Linux32-8 | 57.4 k | 66.0 | 870 | ||
| Linux64-512 | ∼120 k | 26.4 | 4.5 k | ||
| Win32-2 | 139.3 k | 127.3 | 1.09 k | ||
| Win64-2 | ∼200 k | 22.9 | 8.7 k | ||
| 20000 2000 0.5 | chr1 | Mac-2 | nomem | 1520.1 | |
| Mac-12 | nomem | 1121.7 | |||
| Linux32-8 | nomem | 4273.9 | |||
| Linux64-512 | ∼950 k | 1553.3 | 610 | ||
| Win32-2 | nomem | 4912.7 | |||
| Win64-2 | nomem | 1205.1 | |||
| 1000g | Mac-2 | nomem | 20.5 k | ||
| Mac-12 | nomem | 14.5 k | |||
| Linux32-8 | nomem | 54.5 k | |||
| Linux64-512 | ∼13000 k | 20.2 k | 640 | ||
| Win32-2 | nomem | 64.5 k | |||
| Win64-2 | nomem | 14.7 k |
This command is used to select a set of genetic markers which are not too highly correlated with one another. The PLINK 1.9 implementation benefits from laziness (i.e. the correlation coefficient between a pair of variants is no longer computed when it is not needed by the main pruning algorithm) and bitwise operations.