SNPEFF(1)

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.