50. TAGVar: A simple, free software tool to annotate genomic variants for clinical review

Abstract

Comprehensive and whole exome NGS panels can generate large amounts of genomic information for a single specimen. This makes these approaches very powerful, however converting raw signals from the NGS instrument into actionable, clinical information requires specialized data pipelines. The expense and expertise required to deploy these pipelines may place NGS testing out of reach for clinics and research groups in low resource settings. TAGVar (Tertiary Analysis of Genomic Variants) is a freely available software tool that facilitates somatic variant classification in both the clinical and research contexts. The application takes VCF formatted genomic variants and outputs HGVS annotations, predicted effect, and links to external variant databases, like dbSNP, gnomAD, ClinVar, COSMIC, and CancerHotspots.org. TAGVar sorts and categorizes variants based on read coverage, variant allele frequency, inferred transcript effect, description in somatic variant databases, or presence in known cancer-related genes as well as additional user-defined criteria. In the clinic, these classifications streamline the identification of reportable variants. In research, the same classification scheme identifies known and novel somatic variants associated with disease. TAGVar has relatively low memory and CPU requirements and does not require a stable internet connection to run. These design features make TAGVar ideal for use in low resource settings.