Module Documentation


Karchin Lab, Johns Hopkins University, wrapped as a module by Ted Liefeld, Mesirov Lab, UCSD School of Medicine.

Algorithm and scientific questions: <support  at cravat dot us>

Module wrapping issues:  Ted Liefeld  < jliefeld at cloud dot ucsd dot edu>


The OpenCRAVAT GenePattern module submits a list of variants to the OpenCRAVAT Server for analysis. OpenCRAVAT is a software 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. OpenCRAVAT 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.


Publication: Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R. "Integrated Informatics Analysis of Cancer-Related Variants." JCO Clinical Cancer Informatics 4 (2020): 310-317. DOI: 10.1200/CCI.19.00132

Documentation: OpenCRAVAT Wiki

Store: Please see the Store tab on the OpenCRAVAT server for a description of each available analysis module.

Tool Description

Input File

  • OpenCRAVAT accepts input files of several different formats. The most common is VCF but it also accepts a simple tab delimited text file as well as 23andMe, Ancestry, and dbSNP formats.
  • Please see the OpenCRAVAT Docs for more information on input file formats.
  • Note the current version of this tool supports only variants in GRCh38 coordinates. The next release of the tool will provide a selection for older genome version (e.g. GRCh37/hg19)

Output Files

  • <Cravat job number>
    The zip file contains the results of OpenCRAVAT annotation in a comma separated text file format. There are several files in the zip file. The file *.variant.csv will have one line per submitted variant and will contain columns with results from each analysis module.
  • <Cravat job number>.html OpenCRAVAT has a functionally rich environment for filtering, sorting and exploring the variants in your results. This link will take you to the results browser for your job on the OpenCRAVAT server.

Example Data

Small sample input files: VCF TXT


GenePattern 3.9.11 or later (dockerized).


Inputs and Outputs

Name Description
data file* Input file in one of the supported OpenCRAVAT input file formats like VCF.
Cravat username* A requirement of this tool is a valid login to the OpenCRAVAT server. If you don't have a login, use the 'Register' link to create one.
Cravat password* The password for the OpenCRAVAT login.
Annotations This panel is used to select the annotation modules that should be run on the variants. Annotation modules are grouped by category like clinical relevance and variant effect prediction. The drop down lists in each category are multi select list so more than one module in each category can be selected. The same module may be found in multiple categories. A detailed description of each module can be found on the Store tab of the OpenCRAVAT server.

Version Comments

Version Release Date Description
1 2020-04-21 Initial Version, developed against OpenCRAVAT Version: 1.7.2