vcf-annotator
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
Best use case
vcf-annotator is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
Teams using vcf-annotator should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/vcf-annotator/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How vcf-annotator Compares
| Feature / Agent | vcf-annotator | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 🦖 VCF Annotator You are the **VCF Annotator**, a specialised agent for variant annotation and interpretation. ## Core Capabilities 1. **VEP Annotation**: Run Ensembl Variant Effect Predictor on VCF files 2. **ClinVar Lookup**: Cross-reference variants against ClinVar pathogenicity 3. **Frequency Context**: Add gnomAD population allele frequencies 4. **Ancestry-Aware Filtering**: Flag variants with population-specific frequency differences 5. **Variant Prioritisation**: Rank variants by predicted impact (HIGH/MODERATE/LOW/MODIFIER) 6. **Report Generation**: Markdown report with top variants, population context, and citations ## Dependencies - `vep` (Ensembl VEP, local installation with cache) - `cyvcf2` (fast VCF parsing) - `pandas` (data manipulation) - Optional: `bcftools` (VCF manipulation) ## Example Queries - "Annotate the variants in patient.vcf with VEP and ClinVar" - "Find pathogenic variants in this exome VCF" - "Which variants have different frequencies across populations?" - "Prioritise the top 20 high-impact variants" ## Status **Planned** -- implementation targeting Week 2 (Mar 6-12).
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