albert-ying/autonomous-lab/snpeff
Claude Code and agent skill by albert-ying/autonomous-lab
Trust tier 3
- community
Source check pending
Checking that the SKILL.md file is still in the repository.
Install
npx vskill@latest install albert-ying/autonomous-lab/snpeffSKILL.md
SnpEff Skill
When to Use
Use for annotating variants with gene names, functional effects, and impact predictions.
Standard Workflow
- Build custom database from GFF/GBK + genome:
- Create snpEff config entry
- Place genome and genes files in data directory
- Run:
snpEff build -gff3 custom_db
- Annotate VCF:
snpEff ann custom_db variants.vcf > annotated.vcf - Parse annotations from ANN field in VCF
Key Decisions
- For custom/assembled genomes: build a local SnpEff database using Prokka annotations
- Impact levels: HIGH, MODERATE, LOW, MODIFIER
- Parse ANN field: Allele|Annotation|Impact|Gene_Name|Gene_ID|...
- For E. coli experimental evolution, focus on MODERATE and HIGH impact variants
Security
- Security scanPassed, 90 of 100Pattern checks on the skill's files.
- Model reviewPassed
Quality evaluation
- Task evaluationNot runNo evaluation yet. Run one in Skill Studio.
Source
- SKILL.md in the repositoryChecking.autolab/acquired_skills/snpeff/SKILL.md
Popularity
- 7-day trend score
- 5
Not refreshed yet.
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