bedtools/bedtools_annotate
Annotate
Coverage
Overlap
BED
GFF
VCF
Description
Annotates the depth and breadth of coverage of features from multiple files.
This tool analyzes how intervals in the input file are covered by features
from one or more annotation files. It reports either the fraction of each
interval covered, the count of overlapping features, or both metrics.
Default behavior: Reports fraction of each input interval covered by features
Multiple files: Can process multiple annotation files simultaneously
Strand options: Supports same-strand, opposite-strand, or strand-agnostic analysis
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file in BED, GFF, or VCF format to be annotated. Each interval in this file will be analyzed for coverage by features from the annotation files. |
--files | file required multiple | One or more annotation files for coverage analysis. **Format:** BED, GFF, or VCF files containing features to analyze **Multiple files:** Use space-separated list or multiple --files flags **Processing:** Each file analyzed separately with results in columns |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output file with annotation results. Contains input intervals with additional columns showing coverage statistics from each annotation file. |
Options
Name | Type & Properties | Description |
|---|---|---|
--names | string multiple | Descriptive names for each annotation file. **Usage:** One name per file in same order as --files **Header:** Names appear in output header line **Format:** Space-separated list or multiple --names flags |
--counts | boolean_true | Report count of overlapping features instead of coverage fraction. **Default output:** Fraction of input interval covered (0.0-1.0) **With --counts:** Integer count of overlapping features **Use case:** When feature count is more relevant than coverage area |
--both | boolean_true | Report both feature counts and coverage fractions. **Output format:** Count followed by fraction for each annotation file **Columns:** Doubles the number of result columns **Use case:** Comprehensive analysis requiring both metrics |
--strand -s | boolean_true | Require same strandedness for overlap detection. Only count overlaps between features on the same strand. Features on opposite strands are ignored. **Default:** Strand-agnostic analysis |
--different_strand -S | boolean_true | Require different strandedness for overlap detection. Only count overlaps between features on opposite strands. Features on the same strand are ignored. **Default:** Strand-agnostic analysis |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.bed"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.2 \
-main-script target/nextflow/bedtools/bedtools_annotate/main.nf \
-params-file params.yaml Relationships
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Current component
bedtools/bedtools_annotatebiobox v0.4.2
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