Variant Pathogenicity Predictor
Integrate REVEL, CADD, PolyPhen and other scores to predict variant pathogenicity.
Usage
python scripts/main.py --variant "chr17:43094692:G:A" --gene "BRCA1"
python scripts/main.py --vcf variants.vcf --output report.json
Parameters
--variant: Variant in format chr:pos:ref:alt--vcf: VCF file with variants--gene: Gene symbol--scores: Prediction scores to use (REVEL,CADD,PolyPhen)
Integrated Scores
- REVEL (Rare Exome Variant Ensemble Learner)
- CADD (Combined Annotation Dependent Depletion)
- PolyPhen-2 (Polymorphism Phenotyping)
- SIFT (Sorting Intolerant From Tolerant)
- MutationTaster
Output
- Pathogenicity classification
- ACMG guideline interpretation
- Individual score breakdown
- Confidence assessment
Risk Assessment
| Risk Indicator | Assessment | Level |
|---|
| ---------------- | ------------ | ------- |
| Code Execution | Python/R scripts executed locally | Medium |
| Network Access | No external API calls | Low |
| File System Access | Read input files, write output files | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Output files saved to workspace | Low |
Security Checklist
- [ ] No hardcoded credentials or API keys
- [ ] No unauthorized file system access (../)
- [ ] Output does not expose sensitive information
- [ ] Prompt injection protections in place
- [ ] Input file paths validated (no ../ traversal)
- [ ] Output directory restricted to workspace
- [ ] Script execution in sandboxed environment
- [ ] Error messages sanitized (no stack traces exposed)
- [ ] Dependencies audited
Prerequisites
No additional Python packages required.
Evaluation Criteria
Success Metrics
- [ ] Successfully executes main functionality
- [ ] Output meets quality standards
- [ ] Handles edge cases gracefully
- [ ] Performance is acceptable
Test Cases
- Basic Functionality: Standard input → Expected output
- Edge Case: Invalid input → Graceful error handling
- Performance: Large dataset → Acceptable processing time
Lifecycle Status
- Current Stage: Draft
- Next Review Date: 2026-03-06
- Known Issues: None
- Planned Improvements:
- Performance optimization
- Additional feature support