bio-clinical-databases-tumor-mutational-burden
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-tumor-mutational-burden --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Ensembl VEP 111+, SnpEff 5.2+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Tumor Mutational Burden **"Calculate TMB from my tumor sequencing data"** → Compute tumor mutational burden as nonsynonymous coding mutations per megabase with proper panel normalization for immunotherapy eligibility assessment. - Python: `cyvcf2` for VCF parsing + variant counting per panel region ## TMB Calculation from VCF (Ensembl VEP 111+) **Goal:** Calculate tumor mutational burden as nonsynonymous coding mutations per megabase from a somatic VCF. **Approach:** Iterate through VCF variants, filter for coding nonsynonymous consequences via VEP/SnpEff annotations, and divide count by panel size. ```python from cyvcf2 import VCF def calculate_tmb(vcf_path, panel_size_mb): '''Calculate TMB (mutations per megabase) Args: vcf_path: Path to somatic VCF panel_size_mb: C
- Version Compatibility
- TMB Calculation from VCF (Ensembl VEP 111+)
- Panel-Specific TMB (Ensembl VEP 111+)
- TMB with Variant Filtering (Ensembl VEP 111+)
- Clinical TMB Thresholds (Ensembl VEP 111+)
- TMB by Variant Type (Ensembl VEP 111+)
- TMB vs MSI Comparison (Ensembl VEP 111+)
- Batch TMB Calculation
- Related Skills
What does the bio-clinical-databases-tumor-mutational-burden skill do?
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-tumor-mutational-burden --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.