# varCADD > --- name: varcadd-pathogenicity description: Variant Scorer keywords: - variant-interpretation - CADD - pathogenicity - genomics - prediction measurable_outcome: Return pathogenicity scores for a VCF of 1000 variants within 2 minutes, flagging top 1% deleterious hits. license: Non-Commercial metadata: author: Genome Medicine 2025 version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - read_file --- # varCADD (Variant Pathogenicity Predictor) Genome-wide pathogenicity prediction leveraging standing variation data to improve accuracy over traditional CADD scores. ## When to Use * **Variant Prioritization**: Ranking candidate variants in rare disease cases. * **VUS Interpretation**: Assessing variants of uncertain significance. * **Research**: Annotating novel variants in population studies. ## Core Capabilities 1. **Score Generation**: Calculate C-scores for SNVs and indels. 2. **Annotation**: Add functional context (conservation, protein domains). 3. **Filtering**: Identify likely pathogenic variants based on thresholds. ## Workflow 1. **Input**: VCF file. 2. **Annotate**: Run varCADD model. 3. **Filter**: Keep variants with Score > X. 4. **Output**: Annotated VCF or ranked table. ## Example Usage **User**: "Score these variants from patient X." **Agent Action**: ```bash varcadd score --input patient.vcf --output scored.vcf ```