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, 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 |