# Varcadd Pathogenicity

> Variant Scorer

- Skill: `fridrichmethod/varcadd-pathogenicity` (Agent Skill)
- Install (CLI): `npx skillmds@latest add fridrichmethod/varcadd-pathogenicity`
- Raw SKILL.md: https://api.skillmd.com/api/skills/fridrichmethod/varcadd-pathogenicity/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: Non-Commercial
- Author: FridrichMethod (https://skillmd.com/u/fridrichmethod)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/fridrichmethod/varcadd-pathogenicity

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# 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
```


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