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

GigaScience

Table 1 –freq times (sec)

Dataset	Machine	PLINK 1.07	PLINK 1.90	Ratio
synth1	Mac-2	7.3	0.24	30
	Mac-12	6.2	0.18	34
	Linux32-2	13.1	0.56	23
	Linux32-8	4.3	0.18	24
	Linux64-512	5.4	0.18	27
	Win32-2	14.3	0.68	21
	Win64-2	9.6	0.33	29
synth2	Mac-2	43.3	0.84	52
	Mac-12	38.2	0.34	110
	Linux32-2	80.1	1.9	42
	Linux32-8	25.2	0.53	48
	Linux64-512	34.1	0.40	85
	Win32-2	83.6	1.3	64
	Win64-2	70.8	0.55	130
chr1snp	Mac-2	52.5	3.5	15
	Mac-12	40.5	1.3	31
	Linux32-2	72.9	10.2	7.15
	Linux32-8	29.7	1.4	21
	Linux64-512	36.8	1.4	26
	Win32-2	104.3	4.5	23
	Win64-2	76.8	2.2	35
chr1	Mac-2	403.9	35.0	11.5
	Mac-12	163.9	5.3	31
	Linux32-2	nomem	65.3
	Linux32-8	134.1	12.8	10.5
	Linux64-512	144.7	5.4	27
	Win32-2	389.2	21.4	18.2
	Win64-2	285.3	8.1	35

This command reports allele frequencies for each variant. The computation is trivial, so the timings just reflect program initialization speed and file I/O efficiency.

ISSN: 2047-217X