Dataset Information
Mendel-GPU: haplotyping and genotype imputation on graphics processing units.
Ontology highlight
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.
SUBMITTER: Chen GK
PROVIDER: S-EPMC3634317 | biostudies-literature | 2012 Nov
REPOSITORIES: biostudies-literature
Publications
Mendel-GPU: haplotyping and genotype imputation on graphics processing units.
Bioinformatics (Oxford, England) 20120905 22
<h4>Motivation</h4>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.<h4>Results</h4>Our graphics processing unit based software delivers haplotyping and imputation accuracies comparable to competing pr ...[more]