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. 2012 Nov 15;28(22):2979-80.
doi: 10.1093/bioinformatics/bts536. Epub 2012 Sep 5.

Mendel-GPU: haplotyping and genotype imputation on graphics processing units

Gary K Chen  1 , Kai Wang, Alex H Stram, Eric M Sobel, Kenneth Lange
Affiliations

Mendel-GPU: haplotyping and genotype imputation on graphics processing units

Gary K Chen et al. Bioinformatics. .

Abstract

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 graphics processing unit based 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/.

Contact: gary.k.chen@usc.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

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References

    1. Altshuler D, et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–1073. - PMC - PubMed
    1. Ayers KL, Lange K. Penalized estimation of haplotype frequencies. Bioinformatics. 2008;24:1596–1602. - PubMed
    1. Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 2007;81:1084–1097. - PMC - PubMed
    1. Browning SR, Browning BL. Haplotype phasing: existing methods and new developments. Nat. Rev. Genet. 2011;12:703–714. - PMC - PubMed
    1. Chen GK. A scalable and portable framework for massively parallel variable selection in genetic association studies. Bioinformatics. 2012;28:719–720. - PMC - PubMed

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