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tmb-msi-calculator

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Tumor mutation burden and microsatellite instability calculation skill for immunotherapy biomarkers

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Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/tmb-msi-calculator/SKILL.md

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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)