VarSeq is a better ANNOVAR, snpEff and VEP

         June 9, 2015

Yes, I said it. “Them be fighting words” you may say.

Well, it’s worth putting a stake in the ground when you have worked hard to have a claim worth staking.

We have explored the landscape, surveyed the ravines and dangerous cliffs, laboriously removed the boulders and even dynamited a few tree stumps.

Stake planted.

Ok, so now I’m going to back off a bit.

ANNOVAR, snpEff and VEP are broadly adopted toolsets with very friendly and responsive authors that engage their communities.

They are also solving a very narrow problem: annotating variant sites.

VCF file in, annotated VCF or text file out.

They are community support, annotations are “you get what you get”, and they provide minimal support for transformation and filtering.

That may be all you need.

VarSeq’s stake is on a much wider domain. We are empowering users to accomplish just about anything you can imagine wanting to do with a VCF file (or more likely, lots of VCF files).

But even for the head-to-head use case of an annotation toolset, VarSeq has a lot going for it:

  • Largest and most up-to-date repository of Public Annotations
  • Attention to details to getting public data right (left-aligning, multi-allelic spitting, data munging useful fields)
  • Advanced and powerful filtering that can be prototyped and refined in a rich UI
  • Both aggregate and focused annotations, such as clinically relevant transcript and HGVS
  • Multiple definable outputs per project (different filter levels, gene-lists etc.)
  • Exports to VCF, Text and Excel
  • Multi-sample support, including family algorithms like compound-het
  • Data transformations including:
    • VCF and gVCF merging
    • Handing multi-allelic sites in a family-aware and somatic-mutation aware manner
    • Breaking down variants to allelic primitives
    • Left-aligning to canonical forms
    • Auto-computed fields like allelic frequency
    • Custom expression to transform and combine any site or sample-level fields

But wait? I thought VarSeq was just a desktop GUI application?

Not anymore.

My Hemizygous Pathogenic OTC Variant

Figure 1: Visualization of Gabe’s pathogenic hemizygous variant in OTC, with some of the many annotations available through Golden Helix.

With our latest VarSeq release, we now bundle VSPipeline, the command line runner that accesses the full power of VarSeq’s algorithms and flexible project template system from any command line context, including your existing bioinformatics pipeline.

We built this with our clinical users in mind, supporting their need to efficiently generate VarSeq projects from their workflow-encoding project templates. Out of their automated pipelines will come fully produced VarSeq projects, ready for the technical and medical staff to jump into variant interpretation and reporting.

But we are finding some labs are just as excited about the other abilities of VSPipeline, such as going from raw VCFs to annotated and filtered per-sample variant lists in hyperlinked enriched multi-tab Excel files in a fully automated pipeline.

Core labs providing sequencing as a service may use VSPipeline to generate annotated VCFs, but also provide a filtered Excel document with a few prioritized lists to investigate. And just as easily, they can add to their deliverable the very compact VarSeq project, which can be opened, explored and have any easily filtered and customizable table exported using VarSeq’s free “Viewer” mode.

We are excited to be offering VSPipeline as an add-on to VarSeq’s affordable subscription licensing model, run locally on your servers on an unlimited number of samples.

So check it out! Contact us at to set up a demo of VarSeq and VSPipeline, and I’d be happy to consult on building the bioinformatics pipeline to match your workflows and output needs.

Join our webcast tomorrow to see VarSeq in action – register here.

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