Many labs already use DRAGEN upstream, but want more control over what happens after variant calling is complete. VSWarehouse 3 connects those outputs to downstream tertiary workflows that labs can automate, configure, and adapt to their own interpretation and reporting process.
Using DRAGEN with VSWarehouse 3: A Better Path to Tertiary Analysis
Many labs already have secondary analysis in place. For Illumina users, that often means DRAGEN outputs stored in BaseSpace. In the earlier posts in this series, we focused on native upstream automation in VSWarehouse 3 (VSW3), including native support for WDL and built-in Sentieon workflows. Those examples highlight one side of the platform: when secondary and tertiary analysis are linked inside the same governed environment, it becomes easier to launch workflows, track inputs and outputs, and move directly into downstream interpretation, reducing turnaround time. While native execution is valuable, many labs want to keep their current upstream secondary analysis process and improve what happens after it finishes.
A better handoff from upstream analysis
For labs using DRAGEN, the approach is straightforward: secondary analysis runs upstream, outputs are stored in BaseSpace, and Warehouse automation pulls the needed files into the workspace so downstream interpretation can begin.
In day-to-day practice, the inefficient part of the workflow is often not alignment or variant calling itself. It is what happens immediately after: identifying the correct files, moving them into the right place, launching the next step, and making sure the interpretation workflow starts with the right inputs. When those transitions depend on too many manual steps, the process becomes harder to standardize and harder to scale. Clinical labs feel that burden in operational overhead and in the difficulty of maintaining a clear and consistent path from upstream processing into case review and reporting.
VSW3 helps by giving that transition more structure. Even when upstream analysis happens elsewhere, Warehouse can still provide a controlled environment for organizing files, launching downstream workflows, and preserving the context around each run. That makes it easier to connect external secondary results to interpretation and reporting without relying on ad hoc file handling or one-off local habits.
Integration with external secondary analysis pipelines
This is also where the broader VSW3 automation model becomes relevant. Tasks and workflows in Warehouse provide a framework for defining parameters, stages, dependencies, outputs, and run history in a way that is reviewable and repeatable. Not every lab needs to start by moving its entire upstream pipeline into Warehouse, but it matters that the platform can support both models: native automation where that makes sense, and integration where that is the better operational fit.
For clinical labs, that flexibility is important. Some teams want to keep the secondary pipeline they already trust while improving the path into case review, interpretation, and reporting. They are not looking for a disruptive rip-and-replace project. They are looking for a better bridge between sequencing outputs and the downstream work that matters most clinically. VSW3 supports that approach by giving labs a way to bring externally generated results into a more governed interpretation environment.
That point is also relevant for labs evaluating downstream platforms more broadly. Some environments are designed as tightly managed end-to-end systems. Others give labs more control over how workflows are configured, how automation is extended, and how tertiary analysis fits into their own process. Golden Helix has long emphasized the second model. For labs already using DRAGEN upstream, that can be an attractive combination: keep the upstream workflow you know, while gaining a more flexible downstream environment for interpretation and reporting.
Connecting secondary and tertiary analysis more effectively
The larger point of this series is that secondary and tertiary analysis work better when they are connected more intentionally. Sometimes that means native workflow execution in VSW3, as in the earlier WDL and Sentieon examples. Sometimes it means bringing externally generated outputs into Warehouse so the downstream process becomes more consistent, easier to manage, and less dependent on manual handoff.
For labs already using DRAGEN and BaseSpace, that is a practical entry point into VSWarehouse 3. You do not need to rebuild your upstream pipeline to improve the path into tertiary analysis. You need a downstream workflow that gives the handoff more structure, more consistency, and a clearer path into interpretation and reporting.
