33. Customize your variant interpretation workflow with OpenCRAVAT

OpenCRAVAT is an open-source modular variant meta-annotator designed to make variant interpretation accessible to a wide audience. The modular design allows researchers to design customized workflows and utilize a diverse set of analysis methods, fostering a personalized approach to variant interpretation. While valuable information about variants is scattered across hundreds of databases and computational variant effect predictors, OpenCRAVAT centralizes access to these tools and makes them available through an easy-to-use interface. Hundreds of tools can be installed using point-and-click or simple command-line statements, and results are combined and presented in a variety of output formats. These tools cater to a broad range of variant types, encompassing germline, somatic, common, rare, coding and non-coding variants. We have recently introduced 'Packages', a new feature that consists of pre-configured combinations of annotators, filters, and output layouts that are focused on specific variant-related questions. For example, the Drug Interaction Package is designed to find pharmacogenomic annotations; the Hereditary Cancer Package finds rare variants in known hereditary cancer genes; and the Splicing Package focuses on variants associated with aberrant splicing. We are now adding support for annotation of large structural variants, comparison of genetic variants across user-defined patient cohorts, and a workflow for annotation of very large (UK-Biobank sized) cohorts in the cloud. To support neoantigen discovery, we provide annotations of epitopes in the Cancer Epitope Database and Analysis Resource (CEDAR). Finally, we provide a Single Variant Report application customized to the needs of molecular tumor boards, to assist oncologists in making treatment decisions.