variant▌

Production-ready VCF processing and variant annotation skill combining local bioinformatics computation with ToolUniverse database integration. Designed to answer bioinformatics analysis questions about VCF data, mutation classification, variant filtering, and clinical annotation.

Systematic variant interpretation using ToolUniverse - from raw variant calls to ACMG-classified clinical recommendations with structural impact analysis.

Comprehensive clinical interpretation of somatic mutations in cancer. Transforms a gene + variant input into an actionable precision oncology report covering clinical evidence, therapeutic options, resistance mechanisms, clinical trials, and prognostic implications.

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

Port existing Semgrep rules to new target languages with applicability analysis and test-driven validation. \n \n Takes an existing Semgrep rule and target languages as input; produces independent rule and test directories for each applicable language \n Requires mandatory applicability analysis per language before porting, rejecting shortcuts like assuming identical patterns across different ASTs \n Enforces test-first methodology: write minimum 2 vulnerable and 2 safe test cases before creatin

Find similar vulnerabilities and bugs across codebases using pattern-based analysis. \n \n Guides a five-step process: understand root cause, create exact match, identify abstraction points, iteratively generalize patterns, and analyze results with confidence/exploitability triage \n Supports ripgrep for quick searches, Semgrep for simple pattern matching, and CodeQL for cross-function data flow analysis \n Includes ready-to-use CodeQL and Semgrep templates for Python, JavaScript, Java, Go, and