Variant Annotation
Annotates VCF variants and normalizes HGVS with public annotators and gnomAD frequencies.
Install
npx skills add maziyarpanahi/openmed --skill annotating-variants -g -a claude-code -y- Repository
- maziyarpanahi/openmed5.8k
- Category
- Data and ML
- Updated
- 4d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 1,886 tokens
- Runs scripts
- No, instructions only
What it does
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 annotated variants with Genomics/Oncology entities and phenotype from openmed.analyze_text. Tools used are free; restricted clinical databases are user-supplied.
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). For GRCh37 use
https://grch37.rest.ensembl.org. Default species is human/homo_sapiens.
import requests
REST = "https://rest.ensembl.org"
HEADERS = {"Content-Type": "application/json", "Accept": "application/json"}
def vep_hgvs(hgvs: str) -> list[dict]:
"""Annotate a single HGVS variant (GET)."""
r = requests.get(f"{REST}/vep/human/hgvs/{hgvs}", headers=HEADERS, timeout=30)
r.raise_for_status()
return r.json()
