snpEff(1) · carta

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)

AUTHOR

This manual page was written by Pierre Gruet <[email protected]> from the Debian project, but may be used by others. Please report possibly missing or misleading information.