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Motivation: The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined withdoi:10.1093/bioinformatics/btu137 pmid:24618464 pmcid:PMC4071205 fatcat:x6dcfudyynfa5pqqnj4ba3sle4