ensembl_vep/vep

variant effect prediction

annotation

genomics

consequence

missense

Description

Variant Effect Predictor (VEP) determines the effect of variants on genes, transcripts, and protein sequences.

VEP annotates variants with:

Consequence types (missense, nonsense, splice site, etc.)
Gene and transcript information
Protein effect predictions (SIFT, PolyPhen)
Population frequencies and clinical significance
Conservation scores and regulatory features

See the VEP documentation for comprehensive usage.

Inputs

Name	Type & Properties	Description
--input_file -i	file required	Input variant file for annotation. Formats: VCF, VEP, variant_identifier, HGVS, ID, region, SPDI Compression: Supports gzip (.gz) and bgzip compressed files
--format	string	Input file format.

Name

Type & Properties

--input_file

-i

file

required

--format

string

Outputs

Name	Type & Properties	Description
--output_file -o	file required output	Output annotated variants to file. Compression: Automatically compress if filename ends with .gz
--vcf	boolean_true	Output results in VCF format. Default: Tab-delimited text format VCF mode: Adds INFO field with VEP annotations

Name

Type & Properties

--output_file

-o

file

required

output

--vcf

boolean_true

Reference Data

Name	Type & Properties	Description
--species	string	Species for annotation.
--assembly	string	Genome assembly version.
--cache	boolean_true	Use cache files for annotation (recommended). Performance: Much faster than database queries Location: Specify with --dir or use default ~/.vep/
--dir	file	Directory containing cache files.
--cache_version	integer	Use specific cache version.
--offline	boolean_true	Enable offline mode (no database connections). Requires: Cache files and FASTA files Use case: Isolated environments or reproducible runs

Name

Type & Properties

--species

string

--assembly

string

--cache

boolean_true

--dir

file

--cache_version

integer

--offline

boolean_true

Annotation Options

Name	Type & Properties	Description
--everything	boolean_true	Shortcut to switch on commonly used options. Includes: --sift, --polyphen, --ccds, --hgvs, --symbol, --numbers, --domains, --regulatory, --canonical, --protein, --biotype, --uniprot, --tsl, --appris, --gene_phenotype, --af, --af_1kg, --af_esp, --af_gnomad, --max_af, --pubmed, --variant_class, --mane
--canonical	boolean_true	Add canonical transcript flag to output. Canonical: Transcript selected as representative for each gene
--ccds	boolean_true	Add CCDS transcript identifiers.
--protein	boolean_true	Add Ensembl protein identifiers.
--symbol	boolean_true	Add gene symbol (e.g., HGNC).
--hgvs	boolean_true	Add HGVS nomenclature for variants.
--sift	string	Add SIFT prediction and/or score.
--polyphen	string	Add PolyPhen prediction and/or score.

Name

Type & Properties

--everything

boolean_true

--canonical

boolean_true

--ccds

boolean_true

--protein

boolean_true

--symbol

boolean_true

--hgvs

boolean_true

--sift

string

--polyphen

string

Frequency Options

Name	Type & Properties	Description
--af	boolean_true	Add global allele frequency from 1000 Genomes.
--af_1kg	boolean_true	Add continental allele frequencies from 1000 Genomes.
--af_gnomad	boolean_true	Add allele frequencies from gnomAD exomes collections.
--max_af	boolean_true	Add maximum observed allele frequency across populations.

Name

Type & Properties

--af

boolean_true

--af_1kg

boolean_true

--af_gnomad

boolean_true

--max_af

boolean_true

Filtering Options

Name	Type & Properties	Description
--pick	boolean_true	Pick one consequence annotation per variant. Selection: Most severe consequence per gene Output: Single annotation line per variant
--pick_allele	boolean_true	Pick one consequence annotation per allele.
--flag_pick	boolean_true	Flag picked consequence with PICK=1.
--per_gene	boolean_true	Use one consequence annotation per gene.
--pick_order	string	Customize annotation selection criteria order.

Name

Type & Properties

--pick

boolean_true

--pick_allele

boolean_true

--flag_pick

boolean_true

--per_gene

boolean_true

--pick_order

string

Output Filtering

Name	Type & Properties	Description
--most_severe	boolean_true	Output only most severe consequence per variant.
--summary	boolean_true	Output only summary of consequences for each variant.
--filter_common	boolean_true	Shortcut to exclude common variants (frequency > 0.01).

Name

Type & Properties

--most_severe

boolean_true

--summary

boolean_true

--filter_common

boolean_true

Advanced Options

Name	Type & Properties	Description
--buffer_size	integer	Number of variants to read at once.
--no_check_variants_order	boolean_true	Permit variants not ordered by position.
--allow_non_variant	boolean_true	Allow non-variant VCF lines through analysis.

Name

Type & Properties

--buffer_size

integer

--no_check_variants_order

boolean_true

--allow_non_variant

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
format: [ "vcf" ]  
output_file: "$id.$key.output_file.txt"  
species: [ "homo_sapiens" ]  
dir: [ "/root/.vep" ]  
buffer_size: [ 5000 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/ensembl_vep/vep/main.nf \  
  -params-file params.yaml

ensembl_vep/vep

Inputs

Outputs

Reference Data

Annotation Options

Frequency Options

Filtering Options

Output Filtering

Advanced Options

Run this component

Relationships

Used by

Uses