snpeff

Name: snpeff
Author: pcingola

Engineering Community

Repo stars 307
License NOASSERTION
Author repo SnpEff

Interpretation is structured for decision-making; original keeps the upstream SKILL.md unchanged.

Decide Fit First

Core job: Run SnpEff, a variant annotation and effect prediction tool for genomic variants. Use when the user wants to annotate VCF files…
Best fit: Use it when the task has reusable inputs, steps, and validation criteria rather than a one-off answer.
Avoid forcing it: If the source lacks commands, platform support, or external-service evidence, keep those fields unknown instead of guessing.

Design Intent

Structure: The skill is organized around “Running”, “Commands”, “Additional Documentation”, showing how the author expects the agent to judge fit, collect context, and produce verifiable output.
Trigger evidence: Prioritize the author’s wording around when to use it, what context to collect, and what output shape to produce.
Evidence boundary: Author text states facts, repository files prove commands and paths, and Fluxly only adds fit, limits, and usage judgment.

How To Use It

Inputs: Provide target material, scope, expected result, forbidden changes, and validation method.
Invocation: Name snpeff directly; if the source includes slash commands, start with the command and then add task context.
Validation: Start small and check whether the result follows “Running / Commands / Additional Documentation” before expanding.

Boundaries And Review

Dependencies: It usually needs no extra API key, so start with a small validation task.
Permissions: Declared permissions include read / write; ask the agent to state file, command, and rollback boundaries before acting.
Quality bar: A useful result names the deliverable, evidence, and next action. Generic prose means the task needs tighter context.

SnpEff

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.

Full documentation: https://pcingola.github.io/SnpEff/

Running

Use the wrapper script at .claude/skills/snpeff/snpeff.sh. It handles JVM memory defaults and argument passthrough. The JAR file is expected at $HOME/snpEff/snpEff.jar.

IMPORTANT: SnpEff output is typically very large (thousands to millions of lines). ALWAYS redirect output to a file. NEVER let output print to stdout, as it will fill the context window and make the conversation unusable.

# Correct: redirect to file
.claude/skills/snpeff/snpeff.sh <command> [options] [arguments] > output.vcf 2> snpeff.log

# WRONG: never do this
.claude/skills/snpeff/snpeff.sh <command> [options] [arguments]

Commands

Command	Description	Docs
`ann` / `eff`	Annotate variants (default command)	commandline, running, input/output
`build`	Build a SnpEff database from reference genome files	build_db, build_db_gff_gtf
`buildNextProt`	Build NextProt database from XML files	commands
`cds`	Compare CDS sequences (database check)	commands
`closest`	Annotate closest genomic region	commands
`count`	Count reads/bases overlapping genomic intervals	commands
`databases`	List available databases	commands
`download`	Download a pre-built database	commands
`dump`	Dump database contents (BED/TXT)	commands
`genes2bed`	Create BED file from gene list	commands
`len`	Calculate genomic length per marker type	commands
`pdb`	Build interaction database from PDB/AlphaFold data	build_pdb
`protein`	Compare protein sequences (database check)	commands
`seq`	Translate DNA sequence to protein	commands
`show`	Show gene/transcript text representation	commands
`translocReport`	Create translocation report with SVG	commands

Additional Documentation

Topic	File
Introduction	introduction
Additional annotations	additionalann
Building regulation databases	build_reg
Cancer samples	cansersamples
FAQ	faq
Human genomes	human_genomes
Integration (GATK, Galaxy)	integration
Output summary	outputsummary
Troubleshooting	troubleshooting
Download & Install	download
Examples	examples
Help	help

Fluxly profile Author and license come from source; runtime, permissions, and network are Fluxly detections or estimates

Fluxly category: Engineering
Author-declared agents: No explicit declaration found; this is not inferred or tested compatibility
Static check: 94 / 100 · heuristic scan, not runtime safety proof
Author / version / license: @pcingola · NOASSERTION
Fluxly token estimate: Lean
Fluxly setup estimate: Plug-and-play
External API key: No requirement detected
Detected OS requirements: Unspecified
Runtime requirements: Unspecified
Detected file/system behavior: Read-only
Write / modify
Detected network behavior: Local-only
Install commands: None (reference only)

Profile is derived at build time from SKILL.md and install vectors. Subject to drift from author intent.

Heads up: 未限定 allowed-tools，默认拥有全部工具权限。

Output preview snpeff.preview

The current SKILL.md does not define a fixed output example.

SKILL.md SKILL.md

# SnpEff

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.

Full documentation: https://pcingola.github.io/SnpEff/

## Running

Use the wrapper script at `.claude/skills/snpeff/snpeff.sh`. It handles JVM memory defaults and argument passthrough. The JAR file is expected at `$HOME/snpEff/snpEff.jar`.

**IMPORTANT: SnpEff output is typically very large (thousands to millions of lines). ALWAYS redirect output to a file. NEVER let output print to stdout, as it will fill the context window and make the conversation unusable.**

```bash
# Correct: redirect to file
.claude/skills/snpeff/snpeff.sh <command> [options] [arguments] > output.vcf 2> snpeff.log

# WRONG: never do this
.claude/skills/snpeff/snpeff.sh <command> [options] [arguments]
```

## Commands

Command | Description | Docs
------- | ----------- | ----
`ann` / `eff` | Annotate variants (default command) | [commandline](docs/commandline.md), [running](docs/running.md), [input/output](docs/inputoutput.md)
`build` | Build a SnpEff database from reference genome files | [build_db](docs/build_db.md), [build_db_gff_gtf](docs/build_db_gff_gtf.md)
`buildNextProt` | Build NextProt database from XML files | [commands](docs/commands.md)
`cds` | Compare CDS sequences (database check) | [commands](docs/commands.md)
`closest` | Annotate closest genomic region | [commands](docs/commands.md)
`count` | Count reads/bases overlapping genomic intervals | [commands](docs/commands.md)
`databases` | List available databases | [commands](docs/commands.md)
`download` | Download a pre-built database | [commands](docs/commands.md)
`dump` | Dump database contents (BED/TXT) | [commands](docs/commands.md)

…

Evidence boundary and execution chain

Author text anchors workflow facts; Fluxly only indexes current sections, terms, files, and commands.

sections -> Running → Commands → Additional Documentation
terms    -> SnpEff is a variant annotation and effect prediction tool. · Use the wrapper script at .claude/skills/snpeff/snpeff.sh. · IMPORTANT: SnpEff output is typically very large (thousands to millions of lines).
files/cmd -> .claude/skills/snpeff/snpeff.sh · $HOME/snpEff/snpEff.jar · ann · eff · build · buildNextProt · cds · closest
body sha256 -> 054d39e8d732