Table 1.

Runtime required for GWIS compared to recent CPU and GPU methods.

Method	Time for nSNP × nsamples		Exhaustive Search
	0.45M × 5K	5M × 10K
CPU Implementation:
(4 cores, 64 bits, 3GHz Intel)
GWIS (1 filter)	2.7 hours*	28 days	Yes
GWIS (3 filters)	10.9 hours*	113 days	Yes
BOOST [31]	23 hours	8 months	Yes
PLINK [53]	89 days	60 years	Yes
RAPID [32]	15 mins	NA	No
SIXPAC [24]	8.0 hours	NA	No
GPU Implementation:
(448 CUDA cores, 1.215 GHz, NVIDIA GTX 470)
GWIS (1 filter)	13 mins*	2.2 days	Yes
GWIS (3 Filters)	22 mins*	3.8 days	Yes
GBOOST [7]	1.4 hours	15 days	Yes
EpiGPU [8]	17 hours	6 months	Yes
SHEsisEPI [9]	28 hours	10 months	Yes
EPIBLASTER [6]	8.9 days	6 years	Yes

Runtime required for GWIS compared to recent CPU and GPU methods. The first column reports results for WTCCC-sized data (450K SNPs, 5K samples) while the second column shows timings for larger recent GWAS (5M SNPs, 10K samples). The rightmost column denotes whether a method performs exhaustive search of all pairs. Filters run by GWIS are ${\chi }^2$ alone or in combination with DSS and SS tests. The times indicated by '*' are actual run times, and all other times are estimated by scaling (see Supplement Section 2 for exact calculations). Runtime for non-exhaustive methods has not been estimated as it is difficult to judge how these methods scale with the number of SNPs and samples.