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name: tmb-msi-calculator description: Tumor mutation burden and microsatellite instability calculation skill for immunotherapy biomarkers allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • clinical-genomics
  • oncology
  • tmb
  • msi graph: domains: [domain:bioinformatics] specializations: [specialization:biomedical-informatics] skillAreas: [skill-area:statistical-analysis, skill-area:data-analysis, skill-area:python-data-pipelines] workflows: [workflow:experiment-design] roles: [role:biomedical-engineer, role:research-scientist]

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TMB-MSI Calculator Skill

Purpose

Calculate tumor mutation burden and microsatellite instability for immunotherapy biomarker assessment.

Capabilities

• TMB calculation from VCF
• MSI status determination
• Neoantigen prediction
• HLA typing integration
• Biomarker thresholds
• Clinical report generation

Usage Guidelines

• Calculate TMB with appropriate normalization
• Determine MSI status accurately
• Predict neoantigens for immunotherapy
• Apply clinical thresholds for reporting
• Generate actionable reports
• Document methodology and thresholds

Dependencies

• TMBcat
• MSIsensor2
• MANTIS

Process Integration

• Tumor Molecular Profiling (tumor-molecular-profiling)