bedtools/bedtools_slop

genomics

intervals

extend

flanking

slop

expand

regions

Description

Extend genomic intervals by adding flanking sequences (slop) to each feature.

bedtools slop increases the size of genomic intervals by adding a specified number
of base pairs to the start and/or end coordinates. The extension can be symmetric
(same on both sides) or asymmetric (different amounts on each side), and can be
strand-aware for directional features.

This tool is commonly used for:

Creating flanking regions around features of interest
Expanding intervals for motif discovery or regulatory analysis
Generating extended regions for ChIP-seq peak calling
Creating buffer zones around genomic features
Preparing regions for downstream intersection analysis
Converting point features to intervals with context

Type

bash_script

License

MIT

Keywords

genomics

intervals

extend

flanking

slop

expand

regions

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_slop/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file containing genomic intervals to extend. Format: BED, GFF, or VCF file Content: Genomic intervals that will be extended with flanking sequences Requirements: Must contain valid genomic coordinates Usage: Each interval will be expanded according to specified parameters
--genome -g	file required	Genome file defining chromosome sizes for boundary constraints. Format: Tab-delimited text file with chromosome names and sizes Content: Each line contains: <chromName><TAB><chromSize> Usage: Prevents extended coordinates from exceeding chromosome boundaries Creation: Can be generated with 'samtools faidx' or UCSC Table Browser Example format: chr1 249250621 chr2 243199373

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with extended genomic intervals. Format: Same format as input file Content: Original intervals with extended coordinates Boundaries: Coordinates clamped to [0, chromosome_length] range

Name

Type & Properties

--output

file

required

output

Extension Options

Name	Type & Properties	Description
--both -b	double	Extend intervals by this number of base pairs in both directions. Usage: Symmetric extension - same amount added to start and end Interaction: Cannot be used together with --left and --right Percentage mode: When --pct is used, this becomes a fraction (e.g., 0.1 = 10%) Boundary handling: Results clamped to valid chromosome coordinates
--left -l	double	Number of base pairs to subtract from the start coordinate. Usage: Extends the interval upstream (toward lower coordinates) Requirement: Must be used together with --right Interaction: Cannot be used with --both parameter Percentage mode: When --pct is used, this becomes a fraction Strand behavior: Modified by --strand option
--right -r	double	Number of base pairs to add to the end coordinate. Usage: Extends the interval downstream (toward higher coordinates) Requirement: Must be used together with --left Interaction: Cannot be used with --both parameter Percentage mode: When --pct is used, this becomes a fraction Strand behavior: Modified by --strand option
--strand_aware -s	boolean_true	Define left and right extensions based on feature strand. Effect: For negative strand features, left extends downstream, right extends upstream Requirements: Input must contain strand information (6th column in BED) Usage: Enables directional, strand-specific extension Default: false (extension based on coordinate direction only)
--percentage -pct	boolean_true	Interpret extension values as fractions of feature length. Effect: Extension distances calculated as fraction × feature_length Example: -b 0.5 extends each feature by 50% of its length in each direction Applications: Proportional extensions, relative scaling Default: false (absolute base pair values)

Name

Type & Properties

--both

-b

double

--left

-l

double

--right

-r

double

--strand_aware

-s

boolean_true

--percentage

-pct

boolean_true

Output Options

Name	Type & Properties	Description
--header	boolean_true	Include the original file header in output. Usage: Preserves metadata and format information from input Applications: Maintaining file structure, format compatibility Formats: Particularly useful for VCF and GFF files Default: false (no header included)

Name

Type & Properties

--header

boolean_true