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Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results

, , ,
1 Department of Biology, University of New Mexico, Albuquerque, NM, USA
2 Sentieon Inc., Mountain View, CA, USA
3 Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM, USA
4 Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, USA
5 Department of Chemical & Nuclear Engineering, University of New Mexico, Albuquerque, NM, USA
DOI
10.7287/peerj.preprints.1672v2
Published
Accepted
Subject Areas
Bioinformatics, Genomics
Keywords
DNA sequencing, Bioinformatics
Copyright
© 2016 Weber et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Weber JA, Aldana R, Gallagher BD, Edwards JS. 2016. Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results. PeerJ PrePrints 4:e1672v2

Abstract

Sentieon DNAseq Software is a suite of tools for running DNA sequencing secondary analyses. The Sentieon DNAseq Software produces identical results to the Genome Analysis Toolkit (GATK) Best Practice Workflow using HaplotypeCaller, with more than a 20-fold increase in processing speed on the same hardware.

This paper presents a benchmark analysis of the GATK and Sentieon DNAseq software packages using publically available datasets from the 1000 genomes database, and includes speed comparisons and output concordance analyses.

Author Comment

This is a preprint submission with an updated abstract to PeerJ Preprints.

Supplemental Information

vcf results for SRR098416

variant call results off running GATK and Sentieon pipelines on sample SRR098416

DOI: 10.7287/peerj.preprints.1672v2/supp-1

vcf results for SRR742200

variant call results off running GATK and Sentieon pipelines on sample

DOI: 10.7287/peerj.preprints.1672v2/supp-2

vcf results for SRR702068

variant call results off running GATK and Sentieon pipelines on sample SRR702068

DOI: 10.7287/peerj.preprints.1672v2/supp-3

Additional Information

Competing Interests

Rafael Aldana and Brendan Gallagher are employed by Sentieon Inc. Rafael Aldana from Sentieon helped design the experiment and write the shell scripts to drive it, and helped write the manuscript. Brendan Gallagher helped write the manuscript. Sentieon Inc. agreed to publish the results.

Author Contributions

Jessica A. Weber conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Rafael Aldana conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Brendan D. Gallagher wrote the paper, reviewed drafts of the paper.

Jeremy S. Edwards analyzed the data, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The raw data sets are publicly available. They were processed with both GATK best practices and Sentieon DNAseq to produce vcf files.

Funding

The authors received no funding for this work.

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