1. Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.
- Author
-
Al-jouie, Abdulrhman, Esfandiari, Mohammadreza, Ramakrishnan, Srividya, and Roshan, Usman
- Subjects
- *
GRAPHICS processing units , *SINGLE nucleotide polymorphisms , *CHI-squared test , *EPISTASIS (Genetics) , *DEGREES of freedom - Abstract
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. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF