Description
Current methods used for representing biological sequence variants allow flexibility, which has created redundancy within variant archives and discordance among variant representation tools. While research methodologies have been able to adapt to this ambiguity, strict clinical standards make it difficult to use this data in what would otherwise be useful clinical interventions. We implemented a specification developed by the GA4GH Variant Modeling Collaboration (VMC), which details a new approach to unambiguous representation of variants at the allelic level, as a haplotype, or as a genotype. Our implementation, called the VMC Test Suite (http://vcfclin.org), offers web tools to generate and insert VMC identifiers into a VCF file and to generate a VMC bundle JSON representation of a VCF file or HGVS expression. A command line tool with similar functionality is also introduced. These tools facilitate use of this standard—an important step toward reliable querying of variants and their associated annotations.
Learning Objective: To spread awareness of ambiguity in variant representation and its consequences as well as highlight important work done to address this issue and demonstrate implementation of those efforts.
Authors:
Michael Watkins (Presenter)
University of Utah
Shawn Rynearson, University of Utah
Alex Henrie, University of Utah
Karen Eilbeck, University of Utah
Presentation Materials: