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.
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. |
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 |
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 |
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 |
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. |
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 Relationships
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Current component
ensembl_vep/filter_vepbiobox v0.4.2
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