Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
Run SnpEff, a variant annotation and effect prediction tool for genomic variants.
Install Snpeff
$ npx skills add pcingola/SnpEff --skill snpeff -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install pcingola/SnpEff snpeff --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/pcingola/SnpEff.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/snpeff .claude/skills/snpeff && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "snpeff" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpeff into .claude/skills/snpeff/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpeff", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpeffType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add pcingola/SnpEff --skill snpeff -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install pcingola/SnpEff snpeff --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/pcingola/SnpEff.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/snpeff .agents/skills/snpeff && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "snpeff" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpeff into .agents/skills/snpeff/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpeff", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add pcingola/SnpEff --skill snpeff -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install pcingola/SnpEff snpeff --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/pcingola/SnpEff.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/snpeff .cursor/skills/snpeff && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "snpeff" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpeff into .cursor/skills/snpeff/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpeff", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/pcingola/SnpEff.git --path .claude/skills/snpeff--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add pcingola/SnpEff --skill snpeff -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install pcingola/SnpEff snpeff --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/pcingola/SnpEff.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/snpeff .gemini/skills/snpeff && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "snpeff" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpeff into .gemini/skills/snpeff/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpeff", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install pcingola/SnpEff snpeffInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add pcingola/SnpEff --skill snpeff -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/pcingola/SnpEff.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/snpeff .github/skills/snpeff && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "snpeff" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpeff into .github/skills/snpeff/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpeff", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add pcingola/SnpEff --skill snpeff -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install pcingola/SnpEff snpeff --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/pcingola/SnpEff.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/snpeff .opencode/skills/snpeff && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "snpeff" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpeff into .opencode/skills/snpeff/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpeff", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
snpeff- GitHub stars
- 313
- Token cost
- ~823 tokens
- SKILL.md length
- 248 words
- Files
- 25
- Skills in repo
- 2
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Run SnpEff, a variant annotation and effect prediction tool for genomic variants.
- The user wants to annotate VCF files
- SKILL.md covers Running, Commands and Additional Documentation
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Build genome databases
What it does
Snpeff is an agent skill from pcingola/SnpEff. Run SnpEff, a variant annotation and effect prediction tool for genomic variants. Use when the user wants to annotate VCF files, build genome databases, or use SnpEff utilities.
Its SKILL.md is about 820 tokens, which your agent loads only when the skill is triggered. The skill folder holds 25 other files (for example `docs/about.md`, `docs/additionalann.md` and `docs/build_db.md`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Genomic variant annotation and functional effect prediction.
When your agent uses it
- The user wants to annotate VCF files
- Build genome databases
- Use SnpEff utilities
Example prompts
- “/snpeff”
Requirements
- Pre-approved tools (allowed-tools): Bash, Read, Grep, Glob
What it can do on your machine
Read from SKILL.md and the folder at commit 1db1599. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves these tools, so the agent can use them without asking each time:
BashReadGrepGlob
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are bash).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
pcingola.github.io
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Snpeff loads about 823 tokens when it runs. Until then it costs about 46 tokens; SKILL.md has 248 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check: notes
The automated check noted patterns worth knowing about, such as sudo or a known installer.
- NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
allowed-tools: Bash, Read, Grep, Glob
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 248 words (~823 tokens).
“SnpEff is a variant annotation and effect prediction tool. It analyzes VCF files and predicts the functional effects of genetic variants (such as amino acid changes) on known genes.”
- name
- snpeff
- allowed-tools
- Bash, Read, Grep, Glob
Files
SKILL.md and 24 other files in .claude/skills/snpeff of pcingola/SnpEff.
- SKILL.md
- docs/about.md
- docs/additionalann.md
- docs/build_db.md
- docs/build_db_gff_gtf.md
- docs/build_pdb.md
- docs/build_reg.md
- docs/cansersamples.md
- docs/commandline.md
- docs/commands.md
- docs/download.md
- docs/examples.md
- docs/faq.md
- docs/help.md
- docs/human_genomes.md
- docs/index.md
- docs/inputoutput.md
- docs/integration.md
- docs/introduction.md
- docs/license.md
- … and 5 more
Open the folder on GitHubat commit 1db1599
Compare with similar skills
Snpeff next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Snpeff this skillpcingola/SnpEff | 313 | — | ~823 | Automated safety check: Notes | Custom licence | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 3 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw | 15k | — | ~923 | Automated safety check: Pass | MIT |
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13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
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Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
MFA Pipeline Orchestrator
aiming-lab/AutoResearchClaw
Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
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More from pcingola/SnpEff
Snpsift
pcingola/SnpEff
Run SnpSift, a toolbox for filtering and manipulating annotated VCF files.
Related
Categories
Questions about Snpeff
What does Snpeff do?
Run SnpEff, a variant annotation and effect prediction tool for genomic variants. Snpeff is an agent skill from pcingola/SnpEff. Run SnpEff, a variant annotation and effect prediction tool for genomic variants.
When should I use Snpeff?
Snpeff fits situations like: the user wants to annotate VCF files; build genome databases; use SnpEff utilities.
How do I install Snpeff in Claude Code?
Run `npx skills add pcingola/SnpEff --skill snpeff -a claude-code`. Or copy the skill folder (.claude/skills/snpeff in pcingola/SnpEff) into .claude/skills/snpeff in your project. Claude Code loads it when a task matches its description.
How do I install Snpeff in Codex?
Run `npx skills add pcingola/SnpEff --skill snpeff -a codex`. Or copy the skill folder (.claude/skills/snpeff in pcingola/SnpEff) into .agents/skills/snpeff in your project. Codex loads it when a task matches its description.
Can I use Snpeff in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add pcingola/SnpEff --skill snpeff -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/snpeff, .gemini/skills/snpeff, .github/skills/snpeff and .opencode/skills/snpeff in your project.
What does Snpeff need to run?
SKILL.md names no scripts, command-line tools or credentials: Snpeff is instructions for the agent only. Its frontmatter pre-approves these tools: Bash, Read, Grep, Glob.
Does Snpeff access the network?
SKILL.md names 1 domain. As links in the text: pcingola.github.io. This is read from the text; nothing was executed.
Is Snpeff safe to install?
Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.
What licence does Snpeff use?
Snpeff has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Snpeff use?
About 823 tokens (SKILL.md is roughly 3.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Snpeff?
Skills that share tags, products or a category with Snpeff: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Snpeff?
pcingola (a GitHub user) maintains it in pcingola/SnpEff, which has 313 GitHub stars. The repository holds 2 skills in this directory. The repository was last updated on March 9, 2026.
Source: pcingola/SnpEff on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.