Motivation: In modern sequencing studies, one can improve the confidence of genotype calls by phasing haplotypes using information from an external reference panel of fully-typed unrelated individuals. However, the computational demands are so high that they prohibit researchers with limited computational resources from haplotyping large-scale sequence data.
Results: Our GPU software delivers haplotyping and imputation accuracies comparable to competing programs at a fraction of the computational cost and peak memory demand.
Availability: Mendel-GPU, our OpenCL software, runs on Linux platforms and is portable across AMD and nVidia GPUs. Users can download both code and documentation at http://code.google.com/p/mendel-gpu/.
Gary K. Chen, Kai Wang, Alex H. Stram, Eric M. Sobel, Kenneth Lange. Mendel-GPU: Haplotyping and genotype imputation on Graphics Processing Units. Bioinformatics, 2012. [doi: 10.1093/bioinformatics/bts536]