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open-cravat website  
Open-CRAVAT is a python package that performs genomic variant interpretation including variant impact, annotation, and scoring. It has a modular architecture with a wide variety of analysis modules that are developed both by the CRAVAT team and the broader variant analysis community. Open-CRAVAT is a product of the Karchin Lab at Johns Hopkins University in collaboration with In Silico Solutions with funding provided by the National Cancer Institute's ITCR program.

Please see: Open-CRAVAT Docs for installation instructions and software documentation.

Check out our landing page at

Environment Modules

Run module spider open-cravat to find out what environment modules are available for this application.

System Variables

  • HPC_OPEN-CRAVAT_DIR - installation directory
  • HPC_OPEN-CRAVAT_BIN - executable directory


If you publish research that uses open-cravat you have to cite it as follows:

Pagel KA et al. Integrated Informatics Analysis of Cancer-Related Variants. JCO Clinical Cancer Informatics 2020 4, 310-317.

In addition, OpenCRAVAT users are encouraged to cite individual annotations used in their study analysis. The source information and citation for each module made available by OpenCRAVAT are described in their corresponding tile in the interactive open store. Or, alternatively, in the yml file within that module’s source directory.