As a new member of Golden Helix’s Field Application Services team, I’ve recently been diving into the capabilities of VarSeq and our broader software suite – an experience every new VarSeq user goes through. If I could schedule a training call with my former self, there are some key points I’d share to help hit the ground running.
Here are five things I wish I knew when getting started with VarSeq!
1. Customizing Filter Chains with OR Logic
One of VarSeq’s most powerful features is the ability to tailor filter chains to your exact needs. Beyond simply stacking filters, you can use filter containers to combine multiple conditions with OR logic.
This is especially helpful if you want to capture variants that meet one strict set of criteria or rescue variants that match an alternate set of qualifications. For example, a traditional ACMG filter workflow is based on assumptions that the variant will be rare or damaging, but there are always exceptions to the rules. An OR logic allows you to leverage other clinical databases with established variant classifications at the same time.
2. Mastering Project and Report Templates
When I was just getting started, I didn’t appreciate how much time a good repertoire of templates can save. Instead of rebuilding filter chains, annotation sources, and reports from scratch, you can start from a project template tailored to your workflow. At the report rendering stage, a few polished report templates can help you flexibly pivot between different audiences without rewriting a word.
For example, when working with VSClinical for germline or somatic interpretation, using a template guarantees that every project starts with the correct annotation sources, filter strategy, and reporting configuration. A polished set of report templates ensures consistency in layout and content and saves a ton of time when managing a high volume of samples.
3. Visualizing Genomic Features in GenomeBrowse
Visualization often reveals details that tables alone can’t. While working through the CNV analysis tutorial, I discovered that read coverage plots could be explored in GenomeBrowse. Plenty of other features, like transcript structure and overlapping annotations, become more intuitive when seen in their genomic context.
Now, I routinely pull up a GenomeBrowse window when working in VarSeq. The intuitive visualizations help identify relevant features and place them in the context of their genomic neighborhoods, like coverage dropouts in low-complexity regions or the presence of known CPIC pharmacogenomic variants in core star allele loci.
4. Discovering the Versatility of VarSeq PGx
Pharmacogenomics (PGx) is a dynamic and rapidly evolving field, and VarSeq PGx (VSPGx) is designed to keep pace. With curated PGx variant databases, VSPGx ensures that updates to interpretation guidelines (like those from CPIC) are quickly reflected in app. Every workflow designed in VarSeq is highly automatable, but PGx takes that to the next level with predefined gene-drug interactions.
For the particularly challenging CYP2D6 gene, Golden Helix provides the CypCall app, which enables accurate star allele calling. These results can then be easily integrated into VarSeq, supporting phenotype predictions that can directly inform clinical reporting.
5. Running the VarSeq Application in VSWarehouse 3
If you’ve been around VarSeq for a while, you may have heard of VSWarehouse as primarily a database management system. That was true in earlier versions, but with VSWarehouse 3 (VSW3), the platform has expanded far beyond that role.
Today, VSW3 isn’t just about storing annotation sources and project data (although that is a feature). It now provides a full VarSeq graphical user interface (GUI) directly in your browser. This means you can launch the VarSeq app inside VSW3 and work exactly as you would on your desktop, while benefitting from centralized project storage, versioning, and team-wide access. Plus, you’ll find that automation capabilities in VSW3 include, in addition to VSPipeline, a suite of other helpful tasks and workflows that make report generation more efficient than ever.
Final Thoughts
Learning a new software platform can feel daunting – especially when the goal is to generate clinical-grade reports. My biggest takeaway as a VarSeq newbie is that you’re not navigating this alone. Behind VarSeq is a dedicated and scientifically rigorous team ready to help, whether you’re a new customer or, like me, a new team member.
The best way to accelerate your learning is to reach out to our responsive and thoughtful support team. We’re here to help you make the most of the platform!