Table 5.
–blocks runtimes (sec)
| Parameters | Dataset | Machine | Haploview 4.2 | PLINK 1.07 | PLINK 1.90 |
|---|---|---|---|---|---|
| –ld-window-kb 500 | synth1 | Mac-2 | nomem | 3198.4 | 1.7 |
| Mac-12 | ∼45 k | 3873.0 | 1.3 | ||
| Linux32-2 | nomem | 5441.1 | 3.4 | ||
| Linux64-512 | ∼57 k | 2323.4 | 2.9 | ||
| Win32-2 | nomem | 9803.4 | 8.9 | ||
| Win64-2 | ∼51 k | 5513.4 | 2.8 | ||
| –ld-window-kb 1000 | synth1 | Mac-2 | nomem | 6185.7 | 2.2 |
| Mac-12 | ∼45 k | 7394.4 | 9.8 | ||
| Linux32-2 | nomem | 9876.8 | 10.0 | ||
| Linux64-512 | ∼57 k | 4462.1 | 3.9 | ||
| Win32-2 | nomem | 18925.7 | 17.3 | ||
| Win64-2 | ∼51 k | 10.3 k | 3.6 | ||
| –ld-window-kb 500 | chr1 | Mac-2 | nomem | ∼2700 k? | 550.9 |
| Mac-12 | nomem | ∼3600 k? | 426.0 | ||
| Linux32-2 | nomem | ∼4300 k? | 1288.4 | ||
| Linux64-512 | ∼440 k? | ∼2600 k? | 1119.7 | ||
| Win32-2 | nomem | ∼17000 k? | 4535.8 | ||
| Win64-2 | nomem | ∼5700 k? | 1037.2 |
This command breaks the genome into estimated “haplotype blocks” which are usually inherited together. The PLINK 1.9 implementation combines optimizations recently developed by Taliun et al. [26] with additional laziness and bit-level parallelism.