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

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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DOI: 10.1186/s13104-015-1392-5


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 .

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
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