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Install in OpenClaw
/install variant-pathogenicity-predictor-1
Description
Integrate REVEL, CADD, PolyPhen scores to predict variant pathogenicity.
Usage Guidance
The included Python script is small and only computes a composite score from three numeric inputs; it does not implement VCF parsing, ACMG interpretation, CONFIG editing, or file-based reports despite SKILL.md claiming those features. Before installing or granting the agent permission to run this skill: (1) review scripts/main.py yourself — it currently only uses CLI flags (--revel, --cadd, --polyphen, --demo) and has no network or file-read behavior; (2) if you expect VCF support or report generation, require the author to provide the actual implementation or updated documentation; (3) run the script in a sandbox or isolated environment (python -m py_compile scripts/main.py and python scripts/main.py --demo) to confirm behavior; (4) avoid giving the agent access to sensitive files or directories until the skill's true I/O behavior is verified; and (5) ask the author to reconcile SKILL.md with the code and to pin dependencies and add tests if you plan to rely on it for clinical or sensitive decisions.
Capability Analysis
Type: OpenClaw Skill
Name: variant-pathogenicity-predictor-1
Version: 1.0.0
The skill is a simple calculator for genetic variant pathogenicity based on numerical scores (REVEL, CADD, PolyPhen). The Python script (scripts/main.py) contains basic arithmetic logic with no network access, file system writes, or suspicious execution patterns, and the SKILL.md instructions are standard for an AI agent without any prompt-injection or exfiltration attempts.
Capability Assessment
Purpose & Capability
The skill's stated purpose (integrate REVEL/CADD/PolyPhen to predict pathogenicity) matches the small script's core behavior (combine three numeric scores into a composite and classification). However, SKILL.md and metadata claim a broader feature set (VCF input, report.json output, ACMG guideline interpretation, multiple integrated scores beyond the three) that the code does not implement. This is a capability mismatch (overpromising).
Instruction Scope
SKILL.md instructs workflows that reference reading VCFs, writing output files, editing a CONFIG block, producing ACMG interpretations, and running more extensive pipelines. The actual script only accepts --revel, --cadd, --polyphen, or --demo and does not read files or produce structured reports. If an agent follows the SKILL.md literally it may attempt to access or modify files/paths that do not exist, leading to unintended file I/O or escalation of access beyond what the code needs.
Install Mechanism
No install spec — instruction-only plus a small included Python script. Nothing is downloaded or extracted. Low install risk.
Credentials
No environment variables, credentials, or config paths are requested. The skill does not ask for external API keys or sensitive tokens, which is proportionate for this functionality.
Persistence & Privilege
The skill is not marked always:true and requests no elevated or persistent privileges. It does not modify other skills or system config. Autonomous invocation is allowed by platform default and is not by itself a red flag here.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install variant-pathogenicity-predictor-1 - After installation, invoke the skill by name or use
/variant-pathogenicity-predictor-1 - Provide required inputs per the skill's parameter spec and get structured output
Version History
v1.0.0
Initial release of variant-pathogenicity-predictor.
- Integrates REVEL, CADD, PolyPhen, SIFT, and MutationTaster scores to predict variant pathogenicity.
- Provides command-line interface for inputting single variants or VCF files, specifying gene and score types.
- Outputs include pathogenicity classification, ACMG guideline interpretation, individual score breakdown, and confidence assessment.
- Includes structured workflow, input validation, error handling, and explicit risk/security assessment.
- No extra Python dependencies required; packaged for reproducible, auditable execution via scripts/main.py.
Metadata
Frequently Asked Questions
What is Variant Pathogenicity Predictor?
Integrate REVEL, CADD, PolyPhen scores to predict variant pathogenicity. It is an AI Agent Skill for Claude Code / OpenClaw, with 90 downloads so far.
How do I install Variant Pathogenicity Predictor?
Run "/install variant-pathogenicity-predictor-1" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.
Is Variant Pathogenicity Predictor free?
Yes, Variant Pathogenicity Predictor is completely free, licensed under MIT-0. You can download, install and use it at no cost.
Which platforms does Variant Pathogenicity Predictor support?
Variant Pathogenicity Predictor is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).
Who created Variant Pathogenicity Predictor?
It is built and maintained by AIpoch (@aipoch-ai); the current version is v1.0.0.
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