Home » Informatics Iron

GPUs for GWAS

January 23, 2012

By Matthew Dublin

Because the computational burden to search for epistasis in genome-wide association study data is often prohibitive, a team from the Roslin Institute at the University of Edinburgh has attempted a powerful and cheap implementation of a search algorithm on GPUs using OpenCL. The team published a paper in Bioinformatics describing the GPU implementation, which achieved a 92 speed up of an exhaustive epistasis scan for a quantitative phenotype.

In their paper, the authors write that "to achieve a comparable computational improvement without a graphics card would require a large compute-cluster, an option that is often financially non-viable. The implementation presented uses OpenCL—an open-source library designed to run on any commercially available GPU and on any operating system."

Their software, called EpiGPU, is open-source and GPU-vendor independent, meaning that it will run on any GPU card.

It can be downloaded here.