---
name: "snpEff"
section: "1"
platform: "linux"
package: "snpeff"
version: "5.2.f+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/snpEff"
---

# snpEff(1)

genetic variant annotation and effect prediction toolbox

## NAME

snpEff - genetic variant annotation and effect prediction toolbox

## SYNOPSIS

**snpEff** \[*command*\] \[*options*\] \[*files*\]

## AVAILABLE COMMANDS

- **\[err\|ann\]**

  Annotate variants / calculate effects (you can use either 'ann' or 'eff', they mean the same). Default: ann (no command or 'ann').

- **build**

  Build a SnpEff database.

- **buildNextProt**

  Build a SnpEff for NextProt (using NextProt's XML files).

- **cds**

  Compare CDS sequences calculated from a SnpEff database to the one in a FASTA file. Used for checking databases correctness.

- **closest**

  Annotate the closest genomic region.

- **count**

  Count how many intervals (from a BAM, BED or VCF file) overlap with each genomic interval.

- **databases**

  Show currently available databases (from local config file).

- **download**

  Download a SnpEff database.

- **dump**

  Dump to STDOUT a SnpEff database (mostly used for debugging).

- **genes2bed**

  Create a bed file from a genes list.

- **len**

  Calculate total genomic length for each marker type.

- **pdb**

  Build interaction database (based on PDB data).

- **protein**

  Compare protein sequences calculated from a SnpEff database to the one in a FASTA file. Used for checking databases correctness.

- **seq**

  Show sequence (from command line) translation.

- **show**

  Show a text representation of genes or transcripts coordinates, DNA sequence and protein sequence.

- **translocReport**

  Create a translocations report (from VCF file).

## OPTIONS

### Generic options

- **-c** , **-config**

  Specify config file. Default: ~/.snpEff/snpEff.config

- **-configOption** name=value

  Override a config file option

- **-d** , **-debug**

  Debug mode (very verbose).

- **-dataDir** \<path\>

  Override data\_dir parameter from config file.

- **-download**

  Download a SnpEff database, if not available locally. Default: true

- **-nodownload**

  Do not download a SnpEff database, if not available locally.

- **-h** , **-help**

  Show this help and exit

- **-noLog**

  Do not report usage statistics to server

- **-t**

  Use multiple threads (implies '-noStats'). Default 'off'

- **-q** , **-quiet**

  Quiet mode (do not show any messages or errors)

- **-v** , **-verbose**

  Verbose mode

- **-version**

  Show version number and exit

### Database options

- **-canon**

  Only use canonical transcripts.

- **-canonList** \<file\>

  Only use canonical transcripts, replace some transcripts using the 'gene\_id       transcript\_id' entries in \<file\>.

- **-interaction**

  Annotate using interactions (requires interaction database). Default: true

- **-interval** \<file\>

  Use a custom interval in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)

- **-maxTSL** \<TSL\_number\>

  Only use transcripts having Transcript Support Level lower than \<TSL\_number\>.

- **-motif**

  Annotate using motifs (requires Motif database). Default: true

- **-nextProt**

  Annotate using NextProt (requires NextProt database).

- **-noGenome**

  Do not load any genomic database (e.g. annotate using custom files).

- **-noExpandIUB**

  Disable IUB code expansion in input variants

- **-noInteraction**

  Disable interaction annotations

- **-noMotif**

  Disable motif annotations.

- **-noNextProt**

  Disable NextProt annotations.

- **-onlyReg**

  Only use regulation tracks.

- **-onlyProtein**

  Only use protein coding transcripts. Default: false

- **-onlyTr** \<file.txt\>

  Only use the transcripts in this file. Format: One transcript ID per line.

- **-reg** \<name\>

  Regulation track to use (this option can be used add several times).

- **-ss** , **-spliceSiteSize** \<int\>

  Set size for splice sites (donor and acceptor) in bases. Default: 2

- **-spliceRegionExonSize** \<int\>

  Set size for splice site region within exons. Default: 3 bases

**-spliceRegionIntronMin** \<int\> Set minimum number of bases for splice site region within intron. Default: 3 bases

**-spliceRegionIntronMax** \<int\> Set maximum number of bases for splice site region within intron. Default: 8 bases

- **-strict**

  Only use 'validated' transcripts (i.e. sequence has been checked). Default: false

**-ud** , **-upDownStreamLen** \<int\> Set upstream downstream interval length (in bases)

## SEE ALSO

**https://pcingola.github.io/SnpEff/se\_introduction/**

## AUTHOR

This manual page was written by Pierre Gruet \<pgt@debian.org\> from the Debian project, but may be used by others. Please report possibly missing or misleading information.