OpenCRAVAT processes data from various popular variant file formats and offers annotations and visualizations for variants. It provides an easier installation process and more annotation tools than similar software, allowing you to fully customize your variant annotation workflow. OpenCRAVAT can be operated through command-line or an interactive GUI to analyze jobs ranging from single variant to a large cohort. Most popular variant formats are supported including: VCF files, HGVS identifiers, Allele Registry IDs, dbSNP rsIDs, 23andme, AncestryDNA, FamilyTree DNA, and standard genomic coordinates.
OpenCRAVAT family
OpenCRAVAT is an open-source software platform designed for comprehensive variant annotation and prioritization. It integrates a wide range of data sources and prediction tools with filters and visualizations. OpenCRAVAT is extensible through modules to include new annotations and data formats. These modules can be developed and published by anyone, and they are freely available to all users. A command line utility, vcfanno is available for high-throughput parallel processing of very large jobs.
MuPIT
MuPIT (Mutation Position Imaging Toolkit) integrates with OpenCRAVAT to provide 3D protein structure visualization of genomic variants. MuPIT enables customized visual exploration of variants in relation to critical protein regions, small molecule ligands, Cancer Genome Atlas (TCGA) somatic mutations, denovo germline mutations, protein-protein interfaces, and 3D hotspots of TCGA somatic mutations.
cravat.us
cravat.us is the original web version of CRAVAT, launched in 2013. It provides high-throughput real-time scoring of variants with VEST4 and CHASM3.1, including scores for indels, premature stop codons, and splice sites, which are not available through OpenCRAVAT’s precomputed scoring tools.