Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results
- 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
- 2016. Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results. PeerJ PrePrints 4:e1672v1 https://doi.org/10.7287/peerj.preprints.1672v1
Abstract
Sentieon DNA Software is a suite of tools that allow running DNA sequencing secondary analysis pipelines. The Sentieon DNA Software produces results identical to the Genome Analysis Toolkit (GATK) Best Practice Workflow using HaplotypeCaller, with more than 20x increase in processing speed on the same hardware. This paper presents a benchmark analysis of both speed comparison and output concordance between using GATK and Sentieon DNA software on publically available datasets from the 100 genomes database.
Author Comment
This is a preprint submission to PeerJ Preprints.
Supplemental Information
vcf results for SRR098416
variant call results off running GATK and Sentieon pipelines on sample SRR098416
vcf results for SRR742200
variant call results off running GATK and Sentieon pipelines on sample
vcf results for SRR702068
variant call results off running GATK and Sentieon pipelines on sample SRR702068