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Table 4 –indep-pairwise runtimes (sec)

From: Second-generation PLINK: rising to the challenge of larger and richer datasets

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  
  1. 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.