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Varcadd pathogenicity

Skill FridrichMethod/awesome-skills/skills/varcadd-pathogenicity

Variant ScorerFrom its SKILL.md

Install
npx -y skills add FridrichMethod/awesome-skills --skill varcadd-pathogenicity

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What its file declares

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The file declares its own license as Non-Commercial. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

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<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <[email protected]> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

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:

varcadd score --input patient.vcf --output scored.vcf
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

What ships with it

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Just SKILL.md. No reference files, no scripts.

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