SNPEFF

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.