bedtools/bedtools_flank

genomics

intervals

flank

upstream

downstream

flanking

regions

Description

Create flanking intervals for each genomic feature.

This tool generates new intervals representing the regions immediately
upstream and/or downstream of existing genomic features. Unlike slop which
extends existing intervals, flank creates entirely new intervals from the
flanking regions.

Type

bash_script

License

MIT

Keywords

genomics

intervals

flank

upstream

downstream

flanking

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

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file with genomic intervals. Format: BED, GFF, VCF file with genomic intervals Usage: Features for which flanking regions will be created
--genome -g	file required	Genome file defining chromosome sizes. Format: Tab-delimited file with chromosome name and size Purpose: Prevents flanks from extending beyond chromosome boundaries Example: chr1\t249250621 Tip: Can use samtools faidx output (.fai file)

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with flanking intervals. Contains new intervals representing the flanking regions of the input features.

Name

Type & Properties

--output

file

required

output

Flanking Options

Name	Type & Properties	Description
--both -b	string	Create flanking intervals using specified distance in both directions. Input: Integer (base pairs) or Float (if used with --pct) Effect: Creates flanks of equal size upstream and downstream Example: "1000" creates 1kb flanks on both sides Mutually exclusive: Cannot use with --left or --right
--left -l	string	Distance for left/upstream flank from original start coordinate. Input: Integer (base pairs) or Float (if used with --pct) Strand-aware: When used with --strand, respects feature orientation Example: "500" creates 500bp upstream flank Requires: Must be used together with --right
--right -r	string	Distance for right/downstream flank from original end coordinate. Input: Integer (base pairs) or Float (if used with --pct) Strand-aware: When used with --strand, respects feature orientation Example: "300" creates 300bp downstream flank Requires: Must be used together with --left

Name

Type & Properties

--both

-b

string

--left

-l

string

--right

-r

string

Flanking Behavior

Name	Type & Properties	Description
--strand -s	boolean_true	Define left and right flanks based on strand orientation. Effect: For negative-strand features, left becomes downstream Example: -l 500 on minus strand starts flank 500bp downstream Default: false (ignore strand)
--percent -pct	boolean_true	Define flanking distances as fraction of feature length. Effect: Distances become proportional to feature size Example: -l 0.5 on 1000bp feature creates 500bp upstream flank Input format: Use decimals (e.g., "0.1" for 10%) Default: false (absolute base pairs)

Name

Type & Properties

--strand

-s

boolean_true

--percent

-pct

boolean_true

Output Options

Name	Type & Properties	Description
--header	boolean_true	Print header from input file prior to results. Effect: Preserves original file header in output Default: false

Name

Type & Properties

--header

boolean_true