dvcrn 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