OpenCRAVAT

OpenCRAVAT integrates diverse computational prediction methods and databases to annotate, score, and prioritize genomic variants and genes for interpretation in cancer, Mendelian, and complex disease research.

Key Features:

• Modular Architecture: Provides a modular architecture that permits addition of analysis modules for annotation, scoring, and ranking.
• Customizable Pipelines: Supports creation of customized analytical pipelines for tailored variant and gene prioritization workflows.
• Comprehensive Resource Catalog: Aggregates databases of genes and variants, phenotype–genotype relationships, algorithms for scoring and ranking genes, and in silico variant effect prediction tools.
• Integration Across Variant Types: Integrates resources and prediction methods covering germline, somatic, common, rare, coding, and non-coding variants.
• Variant Prioritization and Scoring: Performs multi-factorial variant prioritization using variant impact annotations and scoring/ranking algorithms.
• Example Workflows: Includes example workflows and case studies demonstrating custom workflows to prioritize genes and variants.

Scientific Applications:

• Cancer Genomics: Supports interpretation of somatic and germline variants in cancer research, including prioritization of diagnostic markers and therapeutic targets.
• Mendelian Disease Analysis: Enables prioritization of causal variants and genes in Mendelian disorders using phenotype–genotype relationships and variant effect predictions.
• Complex and Polygenic Conditions: Applicable to analysis of complex polygenic conditions involving common and rare variants.
• Germline and Somatic Mutation Analysis: Facilitates analysis and comparative interpretation of both germline and somatic mutations.

Methodology:

Integrates multiple annotation resources and computational prediction methods to prioritize variants by computing variant impact annotations and applying scoring and ranking algorithms.