Chi8: a GPU program for detecting significant interacting SNPs with the
chi-square 8-df test
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 hours 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.
Citation: Abdulrhman Aljouie, Mohamadreza Esfandiari, Srividya Ramakrishnan and Usman
Chi8: a GPU program for detecting significant interacting SNPs with the chi-square 8-df test,
accepted to BMC research notes, 2015
( Supplementary material )