snpEff1
Genetic variant annotation and effect prediction toolbox
Usage
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)