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Variant Pathogenicity Predictor
by
EC-cyber258
· GitHub ↗
· v0.1.0
· MIT-0
273
Downloads
0
Stars
0
Active Installs
1
Versions
Install in OpenClaw
/install variant-pathogenicity-predictor
Description
Integrate REVEL, CADD, PolyPhen scores to predict variant pathogenicity
Usage Guidance
This skill appears to be a draft with mismatched documentation and implementation. The code itself is simple and low-risk (no network, no credentials), but SKILL.md promises VCF parsing, gene context, and integration of additional predictors that are not implemented. Before installing or trusting results: (1) do not use this for clinical decisions — tests and validation are missing; (2) ask the author for the intended implementation or an updated release that actually parses VCFs and documents dependencies; (3) insist on input validation and path sanitization if file I/O is added; (4) inspect and test any future code that adds network calls or external data sources. Given the inconsistencies, treat this as incomplete/deceptive rather than malicious, but avoid relying on it until it is corrected and properly audited.
Capability Analysis
Type: OpenClaw Skill
Name: variant-pathogenicity-predictor
Version: 0.1.0
The skill is a straightforward bioinformatics tool designed to calculate variant pathogenicity scores based on user-provided numeric inputs. The Python script (scripts/main.py) contains only basic arithmetic logic and lacks any high-risk capabilities such as network access, file system manipulation, or shell execution. No evidence of malicious intent, data exfiltration, or prompt injection was found.
Capability Assessment
Purpose & Capability
Name/description claim integrating REVEL, CADD, PolyPhen and 'other scores' and support for VCF/variant/gene inputs. The actual script only accepts numeric --revel, --cadd, --polyphen flags (and --demo) and returns a simple composite — it does not parse VCFs, handle gene context, or call SIFT/MutationTaster. The declared capabilities are therefore disproportionate to the delivered code.
Instruction Scope
SKILL.md shows CLI usage for --variant, --vcf, --gene and output report.json and includes a security checklist expecting input validation and file I/O protections, but scripts/main.py does none of that. The runtime instructions would lead users to expect file reading/writing and VCF processing that the code doesn't perform — a scope mismatch that could confuse users and lead to improper use.
Install Mechanism
No install spec and only a small Python script with standard-library usage (argparse/json). No external downloads or package installs are required, which is proportionate to the actual shipped code.
Credentials
The skill requests no environment variables, credentials, or config paths. That matches the provided script which runs locally and does not perform network access or require secrets.
Persistence & Privilege
No special persistence or elevated privileges requested (always: false, no installs). The skill does not modify system or other skill configuration.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install variant-pathogenicity-predictor - After installation, invoke the skill by name or use
/variant-pathogenicity-predictor - Provide required inputs per the skill's parameter spec and get structured output
Version History
v0.1.0
Initial release: Variant Pathogenicity Predictor
- Integrates REVEL, CADD, PolyPhen-2, SIFT, and MutationTaster scores to assess genetic variant pathogenicity.
- Supports single variant and VCF file input; outputs pathogenicity classification, ACMG interpretation, score breakdown, and confidence assessment.
- Local script execution with no external API calls; reads input files and writes output reports.
- Includes explicit risk assessment and security checklist.
- No extra dependencies required.
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 273 downloads so far.
How do I install Variant Pathogenicity Predictor?
Run "/install variant-pathogenicity-predictor" 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 EC-cyber258 (@ec-cyber258); the current version is v0.1.0.
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