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

• Published in: Bioinformatics 2012-11, Vol.28 (22), p.2979-2980
• Main Authors: CHEN, Gary K, KAI WANG, STRAM, Alex H, SOBEL, Eric M, LANGE, Kenneth
• Format: Article
• Language: English
• Subjects: Algorithms; Applications Note; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; General aspects; Genome, Human; Genome-Wide Association Study; Genotype; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Polymorphism, Single Nucleotide; Sequence Analysis, DNA; Software
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/bts536

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. 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. 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/. [e-mail]. Supplementary data are available at Bioinformatics online.