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

Type

bash_script

License

MIT

Keywords

Annotate

Coverage

Overlap

BED

GFF

VCF

Links

Repository

Documentation

Contributors

Launch

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 v0.4.1 \  
  -main-script target/nextflow/bedtools/bedtools_annotate/main.nf \  
  -params-file params.yaml

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

Name

Type & Properties

--input

-i

file

required

--files

file

required

multiple

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.

Name

Type & Properties

--output

file

required

output

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

Name

Type & Properties

--names

string

multiple

--counts

boolean_true

--both

boolean_true

--strand

-s

boolean_true

--different_strand

-S

boolean_true