Cutevariant is a graphical user interface (GUI)-based desktop application designed to filter variations from annotated VCF file. The application imports data into a local SQLite database where complex filter queries can be built either from GUI controllers or using a domain-specific language called Variant Query Language. Cutevariant provides more features than existing applications and is fully customizable thanks to a complete plugins architecture.;Cutevariant is distributed as a multiplatform client-side software under an open source license and is available at https://github.com/labsquare/cutevariant.