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Bioinformatics. 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.

Author information

1
Department of Preventive Medicine, USC, Los Angeles, CA 90089, USA. gary.k.chen@usc.edu

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.

PMID:
22954633
PMCID:
PMC3634317
DOI:
10.1093/bioinformatics/bts536
[Indexed for MEDLINE]
Free PMC Article

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