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snpeff-variant-annotation

75 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.

By BioTender-max/awesome-bio-agent-skills (GitHub) · coding · 219 stars · scanned at commit 8cbdd18

Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl VEP for REST API; SnpEff for fast CLI with pre-built genomes.

Works with any agent that supports SKILL.md skills.

What this skill can do

Safer alternatives

Low-risk skills in the same category (coding) that look related. Check that one does what you need.

• 80 Low riskbcftools-variant-manipulationjaechang-hits/SciAgent-Skills · 388 stars
• 100 Low riskvep-variant-annotatora5c-ai/babysitter · 1,903 stars
• 95 Low riskbio-population-genetics-rare-variant-associationlilinji/GeneTind-Life-Skills · 17 stars

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'snpeff-variant-annotation' ] || [ -L ~/.agents/skills/'snpeff-variant-annotation' ]; then echo 'A skill folder named snpeff-variant-annotation already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/sciagent/snpeff-variant-annotation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sciagent/snpeff-variant-annotation' ~/.agents/skills/'snpeff-variant-annotation' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'snpeff-variant-annotation' ~/.claude/skills/'snpeff-variant-annotation' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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