| SNPEFF(1) | User Commands | 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¶
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.
| February 2021 | snpEff |