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Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.
- Source :
-
BMC Research Notes . 9/15/2015, Vol. 8 Issue 1, p1-7. 7p. 5 Diagrams, 7 Charts. - Publication Year :
- 2015
-
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]
Details
- Language :
- English
- ISSN :
- 17560500
- Volume :
- 8
- Issue :
- 1
- Database :
- Academic Search Index
- Journal :
- BMC Research Notes
- Publication Type :
- Academic Journal
- Accession number :
- 109489924
- Full Text :
- https://doi.org/10.1186/s13104-015-1392-5