annotating-variants
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and the clinical context OpenMed extracts. Use when the user wants to predict variant consequences, map HGVS to genomic coordinates, annotate a VCF, attach allele frequencies, or pair variants with phenotype/oncology context. Trigger keywords: VCF, HGVS, variant annotation, VEP, SnpEff, ANNOVAR, consequence, missense, gnomAD, allele frequency, GRCh38, rsID, transcript. Pairs adjacent to OpenMed: combine a
npx skills add maziyarpanahi/openmed --skill annotating-variants --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.
# Annotating variants & normalizing HGVS Turn raw genomic variants — VCF rows, rsIDs, or **HGVS** strings — into annotated, consequence-predicted records, and link them to the **clinical context** OpenMed extracts from text (genes, variants, oncology findings, phenotype). The workhorse for a quick, no-install annotation is the **Ensembl VEP REST API**; for scale, run **VEP**, **SnpEff**, or **ANNOVAR** offline. These annotators are **free and license-permissive**. Restricted clinical interpretation databases (e.g. licensed HGMD) are **user-supplied** — this skill sticks to open resources (Ensembl, gnomAD, ClinVar). ## When to use - You have a VCF / HGVS / rsID and need consequence predictions (missense, stop-gain, splice), affected transcripts, and protein change. - You need to **normalize HGVS** to genomic coordinates (and back) on a known build (GRCh38 by default; GRCh37 via the dedicated endpoint). - You want **gnomAD** population allele frequencies to flag common vs rare. - You are pairing molecular findings with the phenotype/oncology context that OpenMed pulls from notes or literature. ## Quick start (real Ensembl VEP REST call) Base URL: `https://rest.ensembl.org` (GRCh38).
- When to use
- Quick start (real Ensembl VEP REST call)
- Population frequencies via gnomAD (GraphQL)
- Offline annotation at scale
- Workflow
- Hand-off to / from OpenMed
- Edge cases & gotchas
- Standards & references
curl 'https://rest.ensembl.org/vep/human/hgvs/ENST00000269305.9:c.215C>G' \
What does the annotating-variants skill do?
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and the clinical context OpenMed extracts. Use when the user wants to predict variant consequences, map HGVS to genomic coordinates, annotate a VCF, attach allele frequencies, or pair variants with phenotype/oncology context. Trigger keywords: VCF, HGVS, variant annotation, VEP, SnpEff, ANNOVAR, consequence, missense, gnomAD, allele frequency, GRCh38, rsID, transcript. Pairs adjacent to OpenMed: combine a
How do I install it?
Run `npx skills add maziyarpanahi/openmed --skill annotating-variants --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 maziyarpanahi/openmed, a repository with 4,851 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.