ensembl_vep/filter_vep

variant effect prediction

filtering

annotation

genomics

post-processing

Description

Filter and post-process VEP output by consequence type, phenotype, clinical significance, and more.

This script filters VEP output files based on various criteria including:

Consequence types and predicted effects
Clinical significance and phenotype associations
Frequency thresholds from population databases
Quality metrics and variant properties

See the Filter VEP documentation for details.

Type

bash_script

License

Apache-2.0

Keywords

variant effect prediction

filtering

annotation

genomics

post-processing

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
format: [ "tab" ]  
output_file: "$id.$key.output_file.txt"  
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/filter_vep/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input_file -i	file required	Input VEP result file to filter. Format: VEP tab-delimited or JSON format output Compression: Supports gzip compressed files (.gz)
--format	string	Specify 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 filtered results to file. Format: Same format as input file Compression: Automatically gzip if filename ends with .gz

Name

Type & Properties

--output_file

-o

file

required

output

Filtering Options

Name	Type & Properties	Description
--filter	string multiple	Add filter condition. Multiple filters are joined with AND. Syntax: field operator value Operators: eq, ne, gt, gte, lt, lte, match, in, is, exists Examples: - "Consequence eq missense_variant" - "MAX_AF lt 0.01" - "IMPACT match HIGH"
--only_matched	boolean_true	In VCF files, only output matched variants. Default behavior: Output all variants, flag matches With flag: Only output variants passing filters

Name

Type & Properties

--filter

string

multiple

--only_matched

boolean_true

Annotation Options

Name	Type & Properties	Description
--ontology	boolean_true	Use Sequence Ontology (SO) to match consequence terms. Enables: Hierarchical matching of consequence types Example: "transcript_variant" matches "missense_variant"
--count -c	boolean_true	Print only a count of matched variants. Output: Single number instead of filtered variants Use case: Quick summary of filter results

Name

Type & Properties

--ontology

boolean_true

--count

-c

boolean_true

Advanced Options

Name	Type & Properties	Description
--force_valid_header	boolean_true	Force output of valid VCF header when using --only_matched. Use case: Ensure downstream tools can parse filtered VCF
--test	integer	Quick test on first n variants.

Name

Type & Properties

--force_valid_header

boolean_true

--test

integer