Sentieon Genomic Tools Webcast Q&A

         May 18, 2017

Yesterday we had an excellent webcast presentation featuring Sentieon’s Dr. Donald Freed. Golden Helix recently partnered with Sentieon to integrate their secondary analysis tools into our software stack, and this presentation is an introduction to their genomic tools. Please check the webcast out here if you missed it! There were a number of questions asked in the live event, so in today’s blog post I wanted to recap the Q&A session.

Question: Can you tell us more about the types of clients that are using Sentieon?

Answer: Sentieon is being used by many academic institutions across the world.  We have quite a few paying academic customers, which really shows the value the Sentieon tools can provide, so even though these users have the free version of GATK as an alternative, they still choose to pay for using the Sentieon software because of its nice deterministic features and the increased performance that the Sentieon tools provide.  It is also used by quite a few industry customers, and this ranges from large pharmaceutical companies to very small startup companies.  In addition, we have users in the clinical space and the Sentieon tools are being used in CLIA labs for diagnostic purposes.

Question: What is Sentieon’s validation process to compare results with GATK?

Answer: Each release of our tools go through a rigorous quality assurance process. In that quality assurance process, we have known results of GATK and what that means is that we ensure that our tools match the results that are provided by the GATK.  GATK is a little bit of a moving target, so if you run the GATK with multiple threads, every time you run the GATK you’ll get slightly different results. For that reason our tools can’t perfectly match the results that are provided by the GATK, but we like to think that our tools perfectly match the result that is intended by the GATK’s mathematical model.

Question: How does Sentieon work with Varseq? How will Golden Helix support the Sentieon solution?

Answer: Sentieon runs as a pipeline tool, and we prefer to run it in a Linux environment. From there we can work with our clients to develop an entire secondary pipeline. The output of that is a VCF file or BAM file, and that’s the natural input for Varseq. We have tested that so it works like a charm. Interestingly enough, this is also a solution that is valuable for our SVS clients, both people working in the human realm or with plants and animals can leverage the solution. In fact, we already have variations in flight, and the analytics will be conducted with SVS.

Question: What is the pricing model for Sentieon?

Answer: Pretty simple model, the Golden Helix model is an license annual fee that includes certain software packages depending on the conversations we have and what the need is.  For Sentieon, there is a package that is probably sufficient for most of our clients that includes a certain number of panel runs, exome runs or whole genome runs.  For our clients that have high-throughput scenarios that have lots of data to analyze, there is a larger configuration and we’re happy to give you details when you reach out. One of our area directors will give you everything you need to make an informed decision.

Question: What is your development plan to keep up with the future updates from Broad/GATK?

Answer:Any features that are added to the GATK tools are also going to be added to the Sentieon tools. Typically, we just add those tools after any of the bugs have been worked out in the GATK which is around 3 months after the GATK initial lease has been produced.  Essentially if any new features come out in the GATK which we think our customer will find useful, we’ll include those features in our next upcoming release.

Question: Is RNAseq variant calling pipeline a part of Sentieon?

Answer: Yes, Sentieon does offer an RNAseq variant calling pipeline.

Question: What type of solution do you intend to provide for data storage?

Answer: The Sentieon genomic tools are just data processing tools so this does not include a solution for data storage.  Sentieon simply provides you the tools so that you can you use to process your own data. Once the software is integrated with VarSeq, the artifacts of the secondary pipeline can go be stored in Golden Helix’s date warehouse (VSWarehouse). So everything that comes in the pipleline to be stored is then subject to be queries and indexing and all that.  We are not providing the server capability but we have, for example,  installed our warehouse in the cloud so a lot of our clients are considering at least a private cloud solution, so that’s a perfect place for everything to go.

If you have any more questions regarding Sentieon or are interested in learning about integrating their tools, please contact us at!

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