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Updated: Apr 3, 2026

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
Published on: December 10, 2012
Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
Abdulrhman Al-jouie1,2, Mohammadreza Esfandiari3, Srividya Ramakrishnan4
1King Abdullah Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, P.O. Box 22490, Riyadh, 11426, Saudi Arabia. aljouieab@ngha.med.sa.
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 9.6 h on a single GPU. We also study the power, false positives, and area under curve of our program on simulated data and provide a comparison to the GBOOST program. Our program source code is freely available from http://www.cs.njit.edu/usman/Chi8.
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