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

• DOI: 10.1101/794297
• Publication Date: 2019-10-07T02:45:14Z
• Authors: Kymberleigh A Pagel; Rick Kim; Kyle Moad; Ben Busby; Lily Zheng; Matthew Hynes-Grace; Collin Tokheim; Michael Ryan; Rachel Karchin
• Keywords: Blueprint

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