Streamlining Genomic Variant Analysis on AnVIL with the VRS Annotator

The VRS Annotator is a powerful new workflow available on the AnVIL platform that enhances the interoperability of genomic variant data by leveraging GA4GH Variation Representation Specification (VRS) identifiers. Developed by the Ellrott Lab at Oregon Health & Science University and the Wagner Lab at Nationwide Children’s Hospital, this tool makes it easier to standardize, annotate, and integrate genomic data with external knowledge bases such as the GA4GH MetaKB.

What Does the VRS Annotator Do?

The VRS Annotator processes Variant Call Format (VCF) files by adding VRS Allele IDs, which are unique, standardized identifiers for genomic variants. By doing so, it enables seamless data exchange across different genomic databases like MetaKB and various tools like the VRS AnVIL Toolkit.

This workflow is particularly useful for researchers working with large-scale genomic datasets who need to harmonize variant data across different platforms. The VRS Annotator is also a key first step for genomics researchers to query variants across AnVIL!

Key Features

• Automated VCF Annotation – The workflow wraps the functionality of the vrs-python vcf_annotator to efficiently annotate VCF files with GA4GH VRS Allele IDs.
• Integration with MetaKB – Enables retrieval of clinical and functional evidence associated with annotated variants, making it easier to link variants to research and clinical interpretations.
• Flexible Configuration – Supports options for computing both reference and alternate alleles, retrieving detailed variant attributes, and working with multiple genome assemblies (e.g., GRCh37 and GRCh38).
• Seamless Execution on AnVIL – Users can run the workflow directly in an AnVIL workspace, simplifying integration into existing genomics pipelines.

How to Get Started

Getting started is as easy as cloning a workspace! The VRS Annotator is available to use as a WDL workflow in the VRS AnVIL workspace. Within the workspace, researchers upload their VCF files, configure the workflow parameters, and generate annotated outputs that are compatible with GA4GH standards. Researchers can use these outputs in ready-to-demo example notebooks and data.

By incorporating the VRS Annotator into genomic research workflows, AnVIL users can improve data interoperability, streamline variant annotation, and enhance downstream analyses with reliable, standardized variant identifiers.

To learn more about the tooling enabled by VRS…

• Youtube Video: Watch as Alex Wagner and Quinn Wai Wong introduce and demo the VRS Annotator on the AnVIL Platform
• VRS Annotator: Dockstore repository for the workflow
• VRS AnVIL Toolkit: Tools to integrate VRS with the AnVIL platform
• GKS AnVIL: Our Github Organization and the latest work on integrating VRS with AnVIL

Getting Involved

• If you would like to contribute, please communicate via GitHub Issues on the VRS AnVIL Toolkit repository
• If you have questions, please visit help.anvilproject.org
• Learn more about workflows here