Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.

Background: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics.

Findings: We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit. We analyze each of the seven WTCCC genome-wide association studies that have about 5000 total case and controls and 400,000 SNPs in an average of 9.