EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards.

Abstract excerpt

MOTIVATION: Hundreds of genome-wide association studies have been performed over the last decade, but as single nucleotide polymorphism (SNP) chip density has increased so has the computational burden to search for epistasis [for n SNPs the computational time resource is O(n(n-1)/2)]. While the theoretical contribution of epistasis toward phenotypes of medical and economic importance is widely discussed,...

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