bio-variant-calling-clinical-interpretation
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling-clinical-interpretation --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: Entrez Direct 21.0+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Clinical Variant Interpretation Prioritize and interpret variants for clinical significance using databases and ACMG/AMP guidelines. ## Interpretation Framework ``` Annotated VCF │ ├── Database Lookup │ ├── ClinVar (clinical assertions) │ ├── OMIM (disease associations) │ └── gnomAD (population frequency) │ ├── Computational Predictions │ ├── SIFT, PolyPhen-2 │ ├── CADD, REVEL │ └── SpliceAI │ ├── ACMG Classification │ └── Pathogenic → Likely Pathogenic → VUS → Likely Benign → Benign │ └── Prioritized Variant List ``` ## ClinVar Annotation **Goal:** Annotate variants with ClinVar clinical significance and filter by pathogenicity. **Approach:** Download the ClinVar VCF, add CLNSIG/CLNDN/CLNREVSTAT fields with bcf
- Version Compatibility
- Interpretation Framework
- ClinVar Annotation
- Download ClinVar
- Annotate with bcftools
- Filter Pathogenic Variants
- ClinVar Significance Levels
- ClinVar Review Status
- InterVar (ACMG Classification)
- Installation
- Run InterVar
- From VCF
- ACMG/AMP Criteria
- Pathogenic Criteria
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi bcftools annotate \ input.vcf.gz -Oz -o with_clinvar.vcf.gz Pathogenic or Likely pathogenic bcftools view -i 'INFO/CLNSIG~"Pathogenic" || INFO/CLNSIG~"Likely_pathogenic"' \ with_clinvar.vcf.gz -Oz -o pathogenic.vcf.gz Exclude benign bcftools view -e 'INFO/CLNSIG~"Benign" || INFO/CLNSIG~"Likely_benign"' \ with_clinvar.vcf.gz -Oz -o not_benign.vcf.gz
What does the bio-variant-calling-clinical-interpretation skill do?
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling-clinical-interpretation --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.