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Sentieon Secondary Analysis

Precision Data for Precision Medicine




Bioinformatics secondary analysis tools that process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy and 100% consistency.



Sentieon provides complete solutions for secondary DNA analysis. Its software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines. The Sentieon tools are deployable on any generic-CPU-based computing system.

Sentieon products are already installed at over 100 sites worldwide. Its products have been extensively tested and validated by numerous customers, and have run through tens of thousands of genome datasets, the majority of which are WGS or WES, with a total of over 2 peta-basepairs of DNA.

Sentieon DNAseq

Sentieon DNAseq implements the same mathematics used in the Broad Institute’s BWA-GATK HaplotypeCaller 3.x Best Practice Workflow pipeline, but with more efficient computing algorithms and enterprise-strength software implementation. Compared to the BWA-GATK pipeline, the Sentieon DNAseq pipeline is 10X faster measured in terms of total core hours for processing from FASTQ to VCF, on the same generic-CPU-based system with no special hardware requirements. This includes a computing efficiency enhancement to BWA-MEM. For aligned-BAM-to-VCF processing, Sentieon DNAseq is 20X-50X faster than GATK. The software is also able to do joint call on over 100K samples together without intermediate file merging, saving time and effort.

Key Features:

  • Identical mathematics as Broad Institute’s BWA-GATK Best Practice Workflow, but over 10X faster FASTQ-to-VCF, 20X-50X faster BAM-to-VCF, measured in core-hours
  • No run-to-run difference, no down-sampling in high coverage regions
  • 100K samples joint-calling without intermediate file merging
  • Pure software solution running on any generic-CPU-based system

Sentieon TNseq

Sentieon TNseq is a tumor-normal pair somatic variant detection product with modes that can match either MuTect (calls SNV in somatic variants) or MuTect2 (MuTect2 is currently in beta release by the Broad Institute; it calls both SNV and INDEL in somatic variants) in the same sense as Sentieon DNAseq matches BWA-GATK: identical mathematics, but more efficient computing algorithms and enterprise-strength software implementation.

Key Features:

  • Identical mathematics as Broad Institute’s Mutect and MuTect2, but over 10X faster FASTQ-to-VCF, measured in core-hours
  • No run-to-run difference, no down-sampling in high coverage regions
  • Pure software solution running on any generic-CPU-based system

White Papers

Learn more about how Sentieon has outperformed alternative methods in benchmark tests, including GATK:

  • The Sentieon Genomics Tools – A fast and accurate solution to variant calling from next-generation sequence data - Read here
  • Sentieon DNA Pipeline for Variant Detection - Read here

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VarSeq ® Software is intended for Investigational Use Only. The performance characteristics of this product have not been established.