Performance of epistasis detection methods in semi-simulated GWAS

BMC Bioinformatics

Table 3 Measured and extrapolated computation time of each method for various commercially available SNP chips and total number of samples in the GWAS

	Method	DSS	GBOOST	IndOR	fastepi	SHEsisEpi
snps	samples (k)
0.6M (Axiom GW EU)	5	48.7 min*	1.8 h*	1.6 h*	13.5 min*	14.2 min*
	15	1.2 h*	5.3 h	4.8 h	32.5 min*	31 min*
	50	8.1 h	17.7 h	15.8 h	2.2 h	2.4 h
	300	2.0 days	4.4 days	4.0 days	13.5 h	14.2 h
	5000	1.1 months	2.5 months	2.2 months	9.4 days	9.9 days
0.7M (OmniExpress)	5	1.1 h	2.4 h	2.2 h	17 min*	19 min*
	15	3.3 h	7.2 h	6.5 h	55.1 min	58.0 min
	50	11.0 h	1.0 days	21.6 h	3.1 h	3.2 h
	300	2.8 days	6.0 days	5.4 days	18.4 h	19.3 h
	5000	1.5 months	3.4 months	3.0 months	12.7 days	13.4 days
1M (Omni1S-8)	5	2 h*	4.9 h	4.4 h	33 min*	35 min*
	15	6.8 h	14.8 h	13.2 h	1.9 h	2.0 h
	50	22.5 h	2.1 days	1.8 days	6.2 h	6.6 h
	300	5.6 days	12.3 days	11.0 days	1.6 days	1.6 days
	5000	3.1 months	6.8 months	6.1 months	26.0 days	27.4 days
2.5M (Omni2.5-8)	5	14.1 h	1.3 days	1.1 days	3.9 h	4.1 h
	15	1.8 days	3.8 days	3.4 days	11.7 h	12.3 h
	50	5.9 days	12.8 days	11.5 days	1.6 days	1.7 days
	300	1.2 months	2.6 months	2.3 months	9.8 days	10.3 days
	5000	1.6 years	3.5 years	3.1 years	5.4 months	5.7 months

Extrapolation based on one Nvidia Tesla K40 with the present implementation. Comutation time measured are indicated with a star

ISSN: 1471-2105