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 majiayu000/claude-skill-registry --skill 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.
# Tumor Mutational Burden ## TMB Calculation from VCF ```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: Capture region size in megabases Returns: TMB value (mutations/Mb) ''' vcf = VCF(vcf_path) mutation_count = 0 for variant in vcf: # Count nonsynonymous coding mutations # Adjust filters based on VCF annotation format if is_coding_nonsynonymous(variant): mutation_count += 1 tmb = mutation_count / panel_size_mb return tmb def is_coding_nonsynonymous(variant): '''Check if variant is coding nonsynonymous Adjust logic based on your VCF annotation tool: - VEP: CSQ field - SnpEff: ANN field - Funcotator: FUNCOTATION field ''' # Example for VEP annotation csq = variant.INFO.get('CSQ', '') if not csq: return False # Check consequence types nonsynonymous = ['missense_variant', 'nonsense', 'frameshift', 'inframe_insertion', 'inframe_deletion', 'stop_gained', 'stop_lost', 'start_lost'] for transcript in csq.split(','): fields = transcript.split('|') consequence = fields[1] if len(fields) > 1 else '' if any(ns in consequence for ns in nonsynonymous): return True return False
- TMB Calculation from VCF
- Panel-Specific TMB
- TMB with Variant Filtering
- Clinical TMB Thresholds
- TMB by Variant Type
- TMB vs MSI Comparison
- 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 majiayu000/claude-skill-registry --skill 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 majiayu000/claude-skill-registry, a repository with 534 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.