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.
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.
Authors: Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham Journal: Am J Hum Genet Date: 2007-07-25 Impact factor: 11.025
Authors: Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean Journal: Nature Date: 2010-10-28 Impact factor: 49.962
Authors: Benjamin B Chu; Eric M Sobel; Rory Wasiolek; Seyoon Ko; Janet S Sinsheimer; Hua Zhou; Kenneth Lange Journal: Bioinformatics Date: 2021-07-21 Impact factor: 6.931
Authors: Chi Song; Gary K Chen; Robert C Millikan; Christine B Ambrosone; Esther M John; Leslie Bernstein; Wei Zheng; Jennifer J Hu; Regina G Ziegler; Sarah Nyante; Elisa V Bandera; Sue A Ingles; Michael F Press; Sandra L Deming; Jorge L Rodriguez-Gil; Stephen J Chanock; Peggy Wan; Xin Sheng; Loreall C Pooler; David J Van Den Berg; Loic Le Marchand; Laurence N Kolonel; Brian E Henderson; Chris A Haiman; Daniel O Stram Journal: PLoS One Date: 2013-02-28 Impact factor: 3.240