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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 PrePrints4:e1672v2https://doi.org/10.7287/peerj.preprints.1672v2
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.
This is a preprint submission with an updated abstract to PeerJ Preprints.
vcf results for SRR098416
variant call results off running GATK and Sentieon pipelines on sample SRR098416