Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies

Table 2 Example of distributing N SNPs to m(m+1)/2 processor cores (P_i, i = 1, m(m+1)/2) for the case where N/m is an integer, where m = N/n = number of subsets of SNPs with each subset having n SNPs (m and n are assumed integers).

Subset 1: SNP₁ ... SNP_n	Subset 2: SNP_n+1... SNP_2n	... ...	Subset m: SNP_n(m-1)+1 ... SNP_N
P₁	P₂	... ...	P_m	Subset 1: SNP₁ ... SNP_n
	P_m+1	... ...	P_2m-1	Subset 2: SNP_n+1... SNP_2n
		... ...	... ...	... ...
			P_m(m+1)/2	Subset m: SNP_n(m-1)+1 ... SNP_N

Each diagonal core receives one subset of n SNPs and computes [3n + 5n(n - 1)/2] tests, and each off-diagonal core receives two subsets of total 2n SNPs and computes 5n² tests.

ISSN: 1471-2105