snpeff

annotation

effect prediction

snp

variant

vcf

Description

Genetic variant annotation, and functional effect prediction toolbox.
It annotates and predicts the effects of genetic variants on genes and
proteins (such as amino acid changes).

Inputs

Name	Type & Properties	Description
--input	file required	Input variants file.
--genome_version	string required	Reference genome version.

Name

Type & Properties

--input

file

required

--genome_version

string

required

Outputs

Name	Type & Properties	Description
--output	file required output	The output file.
--summary	file output	Summary file directory.
--genes	file output	Txt file directory.

Name

Type & Properties

--output

file

required

output

--summary

file

output

--genes

file

output

Options

Name	Type & Properties	Description
--chr	string	Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
--classic	boolean_true	Use old style annotations instead of Sequence Ontology and Hgvs.
--csv_stats	file	Create CSV summary file.
--download	boolean_true	Download reference genome if not available.
--input_format -i	string	Input format [ vcf, bed ]. Default: VCF. example: "VCF"
--file_list	boolean_true	Input actually contains a list of files to process.
--output_format -o	string	Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
--stats -s --htmlStats	boolean_true	Create HTML summary file.
--no_stats	boolean_true	Do not create stats (summary) file.

Name

Type & Properties

--chr

string

--classic

boolean_true

--csv_stats

file

--download

boolean_true

--input_format

-i

string

--file_list

boolean_true

--output_format

-o

string

--stats

-s

--htmlStats

boolean_true

--no_stats

boolean_true

Results filter options

Name	Type & Properties	Description
--fi --filterInterval	file	Only analyze changes that intersect with the intervals specified in this file. This option can be used several times.
--no_downstream	boolean_true	Do not show DOWNSTREAM changes
--no_intergenic	boolean_true	Do not show INTERGENIC changes.
--no_intron	boolean_true	Do not show INTRON changes.
--no_upstream	boolean_true	Do not show UPSTREAM changes.
--no_utr	boolean_true	Do not show 5_PRIME_UTR or 3_PRIME_UTR changes.
--no	string	Do not show 'EffectType'. This option can be used several times.

Name

Type & Properties

--fi

--filterInterval

file

--no_downstream

boolean_true

--no_intergenic

boolean_true

--no_intron

boolean_true

--no_upstream

boolean_true

--no_utr

boolean_true

--no

string

Annotations options

Name	Type & Properties	Description
--cancer	boolean_true	Perform 'cancer' comparisons (Somatic vs Germline).
--cancer_samples	file	Two column TXT file defining 'original \t derived' samples.
--fastaprot	file	Create an output file containing the resulting protein sequences.
--format_eff	boolean_true	Use 'EFF' field compatible with older versions (instead of 'ANN').
--gene_id	boolean_true	Use gene ID instead of gene name (VCF output).
--hgvs	boolean_true	Use HGVS annotations for amino acid sub-field.
--hgvs_old	boolean_true	Use old HGVS notation.
--hgvs1_letter_aa	boolean_true	Use one letter Amino acid codes in HGVS notation.
--hgvs_tr_id	boolean_true	Use transcript ID in HGVS notation.
--lof	boolean_true	Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-no_hgvs	boolean_true	Do not add HGVS annotations.
--no_lof	boolean_true	Do not add LOF and NMD annotations.
--no_shift_hgvs	boolean_true	Do not shift variants according to HGVS notation (most 3prime end).
--oicr	boolean_true	Add OICR tag in VCF file.
--sequence_ontology	boolean_true	Use Sequence Ontology terms.

Name

Type & Properties

--cancer

boolean_true

--cancer_samples

file

--fastaprot

file

--format_eff

boolean_true

--gene_id

boolean_true

--hgvs

boolean_true

--hgvs_old

boolean_true

--hgvs1_letter_aa

boolean_true

--hgvs_tr_id

boolean_true

--lof

boolean_true

-no_hgvs

boolean_true

--no_lof

boolean_true

--no_shift_hgvs

boolean_true

--oicr

boolean_true

--sequence_ontology

boolean_true

Generic options

Name	Type & Properties	Description
--config -c	file	Specify config file
--config_option	string	Override a config file option (name=value).
--debug -d	boolean_true	Debug mode (very verbose).
--data_dir	file	Override data_dir parameter from config file.
--no_download	boolean_true	Do not download a SnpEff database, if not available locally.
--no_log	boolean_true	Do not report usage statistics to server.
--quiet -q	boolean_true	Quiet mode (do not show any messages or errors)
--verbose -v	boolean_true	Verbose mode.

Name

Type & Properties

--config

-c

file

--config_option

string

--debug

-d

boolean_true

--data_dir

file

--no_download

boolean_true

--no_log

boolean_true

--quiet

-q

boolean_true

--verbose

-v

boolean_true

Database options

Name	Type & Properties	Description
--canon	boolean_true	Only use canonical transcripts.
--canon_list	file	Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in <file>.
--tag	string	Only use transcript having a tag 'tagName'. This option can be used multiple times.
--no_tag	boolean_true	Filter out transcript having a tag 'tagName'. This option can be used multiple times.
--interaction	boolean_true	Annotate using interactions (requires interaction database).
--interval	file	Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).
--max_tsl	integer	Only use transcripts having Transcript Support Level lower than <TSL_number>.
--motif	boolean_true	Annotate using motifs (requires Motif database).
--nextprot	boolean_true	Annotate using NextProt (requires NextProt database).
--no_genome	boolean_true	Do not load any genomic database (e.g. annotate using custom files).
--no_expand_iub	boolean_true	Disable IUB code expansion in input variants.
--no_interaction	boolean_true	Disable inteaction annotations.
--no_motif	boolean_true	Disable motif annotations.
--no_nextprot	boolean_true	Disable NextProt annotations.
--only_reg	boolean_true	Only use regulation tracks.
--only_protein	boolean_true	Only use protein coding transcripts.
--only_tr	file	Only use the transcripts in this file. Format: One transcript ID per line.
--reg	string	Regulation track to use (this option can be used add several times).
--ss --spliceSiteSize	integer	Set size for splice sites (donor and acceptor) in bases. Default: 2.
--splice_region_exon_size	integer	Set size for splice site region within exons. Default: 3 bases.
--splice_region_intron_min	integer	Set minimum number of bases for splice site region within intron. Default: 3 bases.
--splice_region_intron_max	integer	Set maximum number of bases for splice site region within intron. Default: 8 bases.
--strict	boolean_true	Only use 'validated' transcripts (i.e. sequence has been checked).
--ud --upDownStreamLen	integer	Set upstream downstream interval length (in bases).

Name

Type & Properties

--canon

boolean_true

--canon_list

file

--tag

string

--no_tag

boolean_true

--interaction

boolean_true

--interval

file

--max_tsl

integer

--motif

boolean_true

--nextprot

boolean_true

--no_genome

boolean_true

--no_expand_iub

boolean_true

--no_interaction

boolean_true

--no_motif

boolean_true

--no_nextprot

boolean_true

--only_reg

boolean_true

--only_protein

boolean_true

--only_tr

file

--reg

string

--ss

--spliceSiteSize

integer

--splice_region_exon_size

integer

--splice_region_intron_min

integer

--splice_region_intron_max

integer

--strict

boolean_true

--ud

--upDownStreamLen

integer

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.vcf"  
summary: "$id.$key.summary.summary_dir"  
genes: "$id.$key.genes.genes_dir"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.1 \  
  -main-script target/nextflow/snpeff/main.nf \  
  -params-file params.yaml

snpeff

Inputs

Outputs

Options

Results filter options

Annotations options

Generic options

Database options

Run this component

Relationships

Used by

Uses