FAQs | OpenCRAVAT

Frequently Asked Questions


How do I cite OpenCRAVAT?

Masica, D. L., Douville, C., Tokheim, C., Bhattacharya, R., Kim, R., Moad, K., ... & Karchin, R. (2017). CRAVAT 4: cancer-related analysis of variants toolkit. Cancer research, 77(21), e35-e38.

In addition, OpenCRAVAT users are encouraged to cite individual annotations used in their study analysis.

How can I cite the annotations and tools included in my 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.

What is the data source version for this annotation source?

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.

How can I filter my variants based upon a list of gene names?

Yes! Within the filter page, simply paste a list of gene IDs separated by space, comma, or newline.

The data resource I’m interested in is not included in the OpenCRAVAT store. Can we add it?

If the data is available to be shared, we encourage the addition of new resources to the store. To add your own resource to the store, first consult the developer tutorial. For more information or support, feel free to contact us at support@cravat.us

Can I share my results with other users?

Yes! The sqlite output file can be shared between different OpenCRAVAT users, and viewed using the command
cravat-view {input_file}.sqlite

Can the tool generate publication-quality visualizations?

Many of the graphical widgets currently allow for the direct export of high resolution png files. To download each file, select the camera icon to the upper right of the widget box.