CtrlK
BlogDocsLog inGet started
Tessl Logo
SkillPublic

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 annotated variants with Genomics/Oncology entities and phenotype from openmed.analyze_text. Tools used are free; restricted clinical databases are user-supplied.

69

Quality

87%

Does it follow best practices?

Run evals on this skill

Adds up to 20 points to the overall score

View guide
SecuritybySnyk

Passed

No findings from the security scan

SKILL.md
Quality
Evals
Security

No security issues found

Scanned

Repository

maziyarpanahi/openmed

Path

skills/annotating-variants/SKILL.md

Audited
Security analysis
Snyk

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.