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.
GenePattern 3.9.11 or later (dockerized).
Inputs and Outputs
|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.|
|1||2020-04-21||Initial Version, developed against OpenCRAVAT Version: 1.7.2|