Search for epistasis, accelerated using graphics cards
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README.md

epiGPU v2.0

The original release is located here: http://sourceforge.net/projects/epigpu/. All the documentation and binaries for Windows, Mac and Linux can be found there.

This is work in progress for version 2. The following changes have been made:

  • Allow missing phenotypic values
  • Allow phenotypes to be specified in separate file
  • Allow multiple platforms

Still to be done:

  • Make major improvements on data handling side
  • Deal exclusively with binary plink files (no conversion to epiGPU format required)
  • Restructure command-line arguments to be similar to plink and gcta

Master branch is stable. To build, just run:

git clone git://github.com/explodecomputer/epiGPU.git
cd epiGPU
make

NOTE

Unfortunately the data handling side of this software needs to be substantially improved.

  • If you are testing the code, please try using at least 2000 SNPs per chromosome, and at least 500 individuals. Using a very small number of SNPs or individuals may lead to problems.
  • There are problems converting larger datasets, i.e. above 4000 individuals and 600,000 SNPs. This will be dealt with as soon as I have time..!