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OpenCRAVAT, an open source collaborative platform for the annotation of human genetic variation

By Kymberleigh A. Pagel, Rick Kim, Kyle Moad, Ben Busby, Lily Zheng, Matthew Hynes-Grace, Collin Tokheim, Michael Ryan, Rachel Karchin

Posted 06 Oct 2019
bioRxiv DOI: 10.1101/794297

PURPOSE: The modern researcher is confronted with hundreds of published methods to interpret genetic variants. There are databases of genes and variants, phenotype-genotype relationships, algorithms that score and rank genes, and in silico variant effect prediction tools. Because variant prioritization is a multi-factorial problem, a welcome development in the field has been the emergence of decision support frameworks, which make it easier to integrate multiple resources in an interactive environment. Current decision support frameworks are typically limited by closed proprietary architectures, access to a restricted set of tools, lack of customizability, web dependencies that expose protected data, or limited scalability. METHODS: We present OpenCRAVAT, a new open source, scalable decision support system for variant and gene prioritization. We have designed the resource catalog to be open and modular to maximize community and developer involvement, and as a result the catalog is being actively developed and growing every month. Resources made available via the store are well-suited for analysis of cancer, as well as Mendelian and complex diseases. RESULTS: OpenCRAVAT offers both command line utility and dynamic GUI, allowing users to install with a single command, easily download tools from an extensive resource catalog, create customized pipelines, and explore results in a richly detailed viewing environment. We present several case studies to illustrate the design of custom workflows to prioritize genes and variants. CONCLUSION: OpenCRAVAT is distinguished from similar tools by its capabilities to access and integrate an unprecedented amount of diverse data resources and computational prediction methods, which span germline, somatic, common, rare, coding and non-coding variants. OpenCRAVAT is freely available at https://opencravat.org .

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