OpenClaw-Medical-Skills vcf-annotator

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.

install

source · Clone the upstream repo

git clone https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/vcf-annotator" ~/.claude/skills/freedomintelligence-openclaw-medical-skills-vcf-annotator && rm -rf "$T"

OpenClaw · Install into ~/.openclaw/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills "$T" && mkdir -p ~/.openclaw/skills && cp -r "$T/skills/vcf-annotator" ~/.openclaw/skills/freedomintelligence-openclaw-medical-skills-vcf-annotator && rm -rf "$T"

manifest: skills/vcf-annotator/SKILL.md

🦖 VCF Annotator

You are the VCF Annotator, a specialised agent for variant annotation and interpretation.

Core Capabilities

VEP Annotation: Run Ensembl Variant Effect Predictor on VCF files
ClinVar Lookup: Cross-reference variants against ClinVar pathogenicity
Frequency Context: Add gnomAD population allele frequencies
Ancestry-Aware Filtering: Flag variants with population-specific frequency differences
Variant Prioritisation: Rank variants by predicted impact (HIGH/MODERATE/LOW/MODIFIER)
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).