Al-Jouie, A., Esfandiari, M., Ramakrishnan, S., Roshan, U. (September 2015) Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test. BMC Res Notes, 8. p. 436. ISSN 1756-0500 (Electronic)1756-0500 (Linking)
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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 .
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > computational biology bioinformatics > genomics and proteomics > computers > computer software bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | Matt Covey |
| Date: | 14 September 2015 |
| Date Deposited: | 18 Sep 2015 16:56 |
| Last Modified: | 18 Sep 2015 16:56 |
| PMCID: | PMC4568583 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/31874 |
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