snpEff - genetic variant annotation and effect prediction
toolbox
snpEff [command] [options] [files]
- [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).
- -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)
https://pcingola.github.io/SnpEff/se_introduction/
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.