VarStack: a Web Tool for Data Retrieval to Interpret Somatic Variants in Cancer
Background and objectiveAdvances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data in cancer from existing databases. MethodsVarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user-interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer (COSMIC), gnomAD, cBioPortal, ClinVar, OncoKB and UCSC Genome browser. It retrieves the data from these databases and returns back to the user in a fraction of the time it would take to manually navigate each site independently. ResultsUsers submit a variant with gene symbol, peptide change, and coding sequence change. They may select a variety of tumor specific studies in cBioportal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as a CSV file. VarStack also has the batch search feature in which user submits a list of variants and download a CSV file with the data from the databases. With the batch search and data download options users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing variant data to the user from multiple databases in an easy-to-export and interpretable format. AvailabilityVarStack is freely available under https://varstack.brown.edu.