bedtools/bedtools_overlap

genomics

overlap

distance

features

intersection

quantification

Description

Compute the amount of overlap or distance between genomic features.

bedtools overlap computes the amount of overlap (positive values) or distance
(negative values) between genome features and reports the result at the end of
the same line. This tool is useful for quantifying the precise overlap between
features from different datasets or for measuring distances between nearby elements.

This tool is commonly used for:

Quantifying overlap between ChIP-seq peaks and genes
Measuring distances between regulatory elements
Computing precise overlap metrics for comparative genomics
Quality control of feature intersection analyses
Post-processing results from bedtools window operations

Type

bash_script

License

MIT

Keywords

genomics

overlap

distance

features

intersection

quantification

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 v0.4.0 \  
  -main-script target/nextflow/bedtools/bedtools_overlap/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file containing genomic features for overlap computation. Format: Tab-delimited file (typically from bedtools window output) Content: Lines with genomic coordinates for which overlap should be computed Usage: Each line should contain start/end coordinates for two features Requirements: Must contain the specified columns for coordinate extraction Special: Use "stdin" for piped input from other bedtools commands

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with overlap/distance values appended. Format: Same as input with additional overlap column Content: Original lines plus computed overlap (positive) or distance (negative) Values: Positive numbers indicate overlap, negative indicate distance Position: Overlap value is appended as the last column

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--cols	string required	Specify columns (1-based) for start and end coordinates of features. Format: Comma-separated list: start1,end1,start2,end2 Usage: Defines which columns contain the coordinates for overlap calculation Order: Must be in the exact order: start1,end1,start2,end2 Example: "2,3,6,7" for typical bedtools window output Requirements: All specified columns must exist in the input

Name

Type & Properties

--cols

string

required