tmb-msi-calculator

# 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)