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) ORCID 0000-0001-9310-4885
Al-Ars, Z. (TU Delft Computer Engineering) ORCID 0000-0001-7670-8572

 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 algorithm
GPU acceleration
memory access
GATK 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
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