Print Email Facebook Twitter Efficient Acceleration of the Pair-HMMs Forward Algorithm for GATK HaplotypeCaller on Graphics Processing Units Title Efficient Acceleration of the Pair-HMMs Forward Algorithm for GATK HaplotypeCaller on Graphics Processing Units Author Ren, S. (TU Delft Computer Engineering) Bertels, K.L.M. (TU Delft FTQC/Bertels Lab; TU Delft Quantum & Computer Engineering) Al-Ars, Z. (TU Delft Computer Engineering) Department Quantum & Computer Engineering Date 2018 Abstract GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to accelerate the pair-HMMs forward algorithm on graphics processing units (GPUs) to improve the performance of GATK HC. This article presents several GPU-based implementations of the pair-HMMs forward algorithm. It also analyzes the performance bottlenecks of the implementations on an NVIDIA Tesla K40 card with various data sets. Based on these results and the characteristics of GATK HC, we are able to identify the GPU-based implementations with the highest performance for the various analyzed data sets. Experimental results show that the GPU-based implementations of the pair-HMMs forward algorithm achieve a speedup of up to 5.47× over existing GPU-based implementations. Subject Pair-HMMs forward algorithmGPU accelerationmemory accessGATK HaplotypeCaller To reference this document use: http://resolver.tudelft.nl/uuid:187fb061-9298-403e-a37b-362ff8e8c922 DOI https://doi.org/10.1177/1176934318760543 ISSN 1176-9343 Source Evolutionary Bioinformatics, 14, 1-12 Part of collection Institutional Repository Document type journal article Rights © 2018 S. Ren, K.L.M. Bertels, Z. Al-Ars Files PDF 1176934318760543.pdf 1.23 MB Close viewer /islandora/object/uuid:187fb061-9298-403e-a37b-362ff8e8c922/datastream/OBJ/view