FAQs | OpenCRAVAT

Frequently Asked Questions


How do I cite OpenCRAVAT?

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.

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.

How can OpenCRAVAT be used for variant prioritization?

OpenCRAVAT does not perform automatic variant prioritization. The annotations, filters, and interface made available by OpenCRAVAT enable custom variant prioritization that takes into account the analysis type, sample size, and phenotype complexity. Here are some examples:

  • Find known and predicted cancer driver mutations from somatic mutations in oncogenes.

  • Identify variants that segregate with disease in a family, and assess the potential for functional impact, prediction scores, and prevalence in population databases.

  • Find genes or variants that are impacted more often than chance in a cohort.

  • Evaluate the impact of variants of unknown significance by comparing multiple forms of evidence.

  • Identify rare variants that occur in the same population-specific haplotype block as known GWAS risk loci.

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.

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 [email protected]

Method developers and researchers can make their results available by packaging them as an OpenCRAVAT annotator and then publishing them to the app store. Annotators typically include a database of annotations for fast high-throughput analysis of large variant files. The preferred storage mechanism for annotator reference data is sqlite databases, but other formats can be used. For more information, consult the annotator tutorial.

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.

What is the licensing model? Are there restrictions on who can use the software or the app store?

OpenCRAVAT is open source and freely available under the MIT license. The majority of annotation data is openly available, as well. There are some exceptions that are not freely available for commercial use including ABRaOM, BRCA1 Assay, CADD, Cancer Gene Census, COSMIC, GRASP, HGDP, LINSIGHT, REVEL, VISTA Enhancer Browser and VEST. These annotation sources have a red warning message in the app store that provides more information and the contact info for licensing. We recommend that users verify the licenses for the datasets used in their analyses, as these may be subject to change.

Can I annotate CNV, SV, repeat or gene fusion events?

While we recognize the biological and clinical importance of these events, OpenCRAVAT is funded to annotate only small-scale variation, under our current grant funding. We hope to expand to annotate these important events in the future.