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)