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.