snpeff

name	snpeff
description	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.
allowed-tools	Bash, Read, Grep, Glob

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