Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Run SnpSift, a toolbox for filtering and manipulating annotated VCF files.
Install Snpsift
$ npx skills add pcingola/SnpEff --skill snpsift -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install pcingola/SnpEff snpsift --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/snpsift .claude/skills/snpsift && 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 "snpsift" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpsift into .claude/skills/snpsift/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpsift", 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/snpsiftType 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 snpsift -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install pcingola/SnpEff snpsift --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/snpsift .agents/skills/snpsift && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "snpsift" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpsift into .agents/skills/snpsift/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpsift", 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 snpsift -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install pcingola/SnpEff snpsift --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/snpsift .cursor/skills/snpsift && 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 "snpsift" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpsift into .cursor/skills/snpsift/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpsift", 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/snpsift--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 snpsift -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install pcingola/SnpEff snpsift --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/snpsift .gemini/skills/snpsift && 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 "snpsift" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpsift into .gemini/skills/snpsift/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpsift", 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 snpsiftInstalls 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 snpsift -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/snpsift .github/skills/snpsift && 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 "snpsift" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpsift into .github/skills/snpsift/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpsift", 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 snpsift -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 snpsift --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/snpsift .opencode/skills/snpsift && 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 "snpsift" agent skill from https://github.com/pcingola/SnpEff/tree/master/.claude/skills/snpsift into .opencode/skills/snpsift/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "snpsift", 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
snpsift- GitHub stars
- 313
- Token cost
- ~851 tokens
- SKILL.md length
- 281 words
- Files
- 34
- Skills in repo
- 2
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Run SnpSift, a toolbox for filtering and manipulating annotated VCF files.
- The user wants to filter variants
- SKILL.md covers Running, Commands and Additional Documentation
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Annotate with databases (dbNSFP
What it does
Snpsift is an agent skill from pcingola/SnpEff. Run SnpSift, a toolbox for filtering and manipulating annotated VCF files. Use when the user wants to filter variants, annotate with databases (dbNSFP, dbSnp, GWAS), extract fields, or manipulate VCF files.
Its SKILL.md is about 850 tokens, which your agent loads only when the skill is triggered. The skill folder holds 34 other files (for example `docs/about.md`, `docs/annotate.md` and `docs/annotate_mem.md`).
It sits in Research & Science. The repository describes itself as: Genomic variant annotation and functional effect prediction.
When your agent uses it
- The user wants to filter variants
- Annotate with databases (dbNSFP
- Manipulate VCF files
Example prompts
- “/snpsift”
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
Snpsift loads about 851 tokens when it runs. Until then it costs about 54 tokens; SKILL.md has 281 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 281 words (~851 tokens).
“SnpSift is a toolbox for filtering and manipulating annotated VCF files. Once genomic variants have been annotated, SnpSift helps filter and process them to find relevant variants.”
- name
- snpsift
- allowed-tools
- Bash, Read, Grep, Glob
Files
SKILL.md and 33 other files in .claude/skills/snpsift of pcingola/SnpEff.
- SKILL.md
- docs/about.md
- docs/annotate.md
- docs/annotate_mem.md
- docs/casecontrol.md
- docs/concordance.md
- docs/dbnsfp.md
- docs/download.md
- docs/examples.md
- docs/extractfields.md
- docs/faq.md
- docs/filter.md
- docs/genesets.md
- docs/gt.md
- docs/gwascatalog.md
- docs/help.md
- docs/index.md
- docs/intersect.md
- docs/intervals.md
- docs/intervalsindex.md
- … and 14 more
Open the folder on GitHubat commit 1db1599
Compare with similar skills
Snpsift 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 |
|---|---|---|---|---|---|---|
| Snpsift this skillpcingola/SnpEff | 313 | — | ~851 | Automated safety check: Notes | Custom licence | |
| Hypothesis Generationspacering-net/codeg | 3.8k | 15 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 83k | 5 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 46k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Read arXiv Paperkarpathy/nanochat | 58k | 2 repos | ~494 | Automated safety check: Pass | MIT | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT |
Similar skills
GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Nature Paper Card
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Read arXiv Paper
karpathy/nanochat
Fetches the TeX source of an arXiv paper from its URL, reads it and writes a markdown summary tied to the nanochat project.
Content Research Writer
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
Peer Review
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
More from pcingola/SnpEff
Snpeff
pcingola/SnpEff
Run SnpEff, a variant annotation and effect prediction tool for genomic variants.
Related
Categories
Questions about Snpsift
What does Snpsift do?
Run SnpSift, a toolbox for filtering and manipulating annotated VCF files. Snpsift is an agent skill from pcingola/SnpEff. Run SnpSift, a toolbox for filtering and manipulating annotated VCF files.
When should I use Snpsift?
Snpsift fits situations like: the user wants to filter variants; annotate with databases (dbNSFP; manipulate VCF files.
How do I install Snpsift in Claude Code?
Run `npx skills add pcingola/SnpEff --skill snpsift -a claude-code`. Or copy the skill folder (.claude/skills/snpsift in pcingola/SnpEff) into .claude/skills/snpsift in your project. Claude Code loads it when a task matches its description.
How do I install Snpsift in Codex?
Run `npx skills add pcingola/SnpEff --skill snpsift -a codex`. Or copy the skill folder (.claude/skills/snpsift in pcingola/SnpEff) into .agents/skills/snpsift in your project. Codex loads it when a task matches its description.
Can I use Snpsift 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 snpsift -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/snpsift, .gemini/skills/snpsift, .github/skills/snpsift and .opencode/skills/snpsift in your project.
What does Snpsift need to run?
SKILL.md names no scripts, command-line tools or credentials: Snpsift is instructions for the agent only. Its frontmatter pre-approves these tools: Bash, Read, Grep, Glob.
Does Snpsift 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 Snpsift 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 Snpsift use?
Snpsift 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 Snpsift use?
About 851 tokens (SKILL.md is roughly 3.4k 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 Snpsift?
Skills that share tags, products or a category with Snpsift: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Snpsift?
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.