bedtools/bedtools_window

genomics

window

proximity

overlap

annotation

neighborhood

bedtools

Description

Examine a "window" around each feature in A and report overlapping features in B.

For each feature in file A, bedtools window searches for overlapping features in
file B within a defined window around each feature in A. The window can be
symmetrical (same distance upstream and downstream) or asymmetrical (different
distances). For each overlap found, the complete entries from both files A and B
are reported.

This tool is particularly useful for:

Finding features within a specific distance of target regions
Associating regulatory elements with nearby genes
Creating annotation contexts around genomic features
Proximity-based genomic analysis
Building feature neighborhoods for downstream analysis

Type

bash_script

License

MIT

Keywords

genomics

window

proximity

overlap

annotation

neighborhood

bedtools

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

Inputs

Name	Type & Properties	Description
--input_a -a	file required	Query file in BED, GFF, or VCF format. Format: BED, GFF, or VCF file with genomic coordinates Content: Features around which windows will be created Usage: Each feature becomes the center of a search window Requirements: Must have valid genomic coordinates
--input_b -b	file required	Database file in BED, GFF, or VCF format. Format: BED, GFF, or VCF file with genomic coordinates Content: Features to search for within windows around A Usage: Features overlapping windows around A will be reported Requirements: Must have matching chromosome names with file A

Name

Type & Properties

--input_a

-a

file

required

--input_b

-b

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with overlapping feature pairs. Format: Tab-separated file with entries from both input files Content: For each overlap, complete records from both A and B files Structure: Columns from A file followed by columns from B file Size: Number of lines depends on overlaps found within windows

Name

Type & Properties

--output

file

required

output

Window Options

Name	Type & Properties	Description
--window_size -w	integer	Base pairs added upstream and downstream of each entry in A. Default: 1000 bp Usage: Creates symmetrical windows around features in A Effect: Extends search region by this amount in both directions Range: Must be positive integer Note: Cannot be used with -l/-r options
--left_window -l	integer	Base pairs added upstream (left) of each entry in A. Default: 1000 bp Usage: Creates asymmetrical windows with custom upstream extension Effect: Extends search region upstream by this amount Range: Must be positive integer Note: Use with -r to create asymmetrical windows
--right_window -r	integer	Base pairs added downstream (right) of each entry in A. Default: 1000 bp Usage: Creates asymmetrical windows with custom downstream extension Effect: Extends search region downstream by this amount Range: Must be positive integer Note: Use with -l to create asymmetrical windows
--strand_windows -sw	boolean_true	Define left (-l) and right (-r) based on strand orientation. Usage: For negative-strand features, -l adds bases downstream Effect: Makes window extensions relative to feature orientation Default: false (extensions are always relative to chromosome coordinates) Requirement: Only works with -l and -r options, not with -w

Name

Type & Properties

--window_size

-w

integer

--left_window

-l

integer

--right_window

-r

integer

--strand_windows

-sw

boolean_true

Strand Options

Name	Type & Properties	Description
--same_strand -sm	boolean_true	Only report overlaps between features on the same strand. Usage: Restricts results to strand-specific overlaps Effect: Features must be on identical strands to be reported Default: false (strand is ignored) Note: Cannot be used with --opposite_strand
--opposite_strand -Sm	boolean_true	Only report overlaps between features on opposite strands. Usage: Restricts results to antisense overlaps Effect: Features must be on opposite strands to be reported Default: false (strand is ignored) Note: Cannot be used with --same_strand

Name

Type & Properties

--same_strand

-sm

boolean_true

--opposite_strand

-Sm

boolean_true

Output Options

Name	Type & Properties	Description
--unique -u	boolean_true	Write the original A entry once if any overlaps found in B. Usage: Reports existence of overlap without listing all B features Effect: Each A feature appears at most once in output Output: Only A file columns, no B file columns Use case: When you only need to know if overlap exists
--count -c	boolean_true	For each entry in A, report the number of overlaps with B. Usage: Adds count column showing number of B features in window Effect: Each A entry gets additional column with overlap count Output: Original A columns plus count column Values: 0 for no overlaps, positive integers for overlap count
--no_overlaps -v	boolean_true	Only report entries in A that have no overlaps with B. Usage: Filters to show only A features with no nearby B features Effect: Inverse of normal operation (like "grep -v") Output: Only A file columns for features with no overlaps Use case: Finding isolated or unique features
--header	boolean_true	Print the header from the A file prior to results. Usage: Preserves header information from input file A Effect: First line of output will be the A file header Default: false (no header in output) Note: Only applicable if A file contains header lines

Name

Type & Properties

--unique

-u

boolean_true

--count

-c

boolean_true

--no_overlaps

-v

boolean_true

--header

boolean_true

BAM Options

Name	Type & Properties	Description
--input_bam -abam	file	Input A file in BAM format instead of BED/GFF/VCF. Format: Sorted BAM file with aligned reads Usage: Replaces -a option for BAM input Output: Default output is BAM format Requirements: Must be coordinate-sorted Note: Cannot be used together with --input_a
--uncompressed_bam -ubam	boolean_true	Write uncompressed BAM output when using BAM input. Usage: Only applicable when using --input_bam Effect: Output BAM will be uncompressed for faster writing Default: false (compressed BAM output) Performance: Faster writing but larger file size
--bed_output -bed	boolean_true	Write output as BED format when using BAM input. Usage: Only applicable when using --input_bam Effect: Converts BAM records to BED format in output Default: false (BAM output when BAM input) Format: Standard BED format with coordinates and names

Name

Type & Properties

--input_bam

-abam

file

--uncompressed_bam

-ubam

boolean_true

--bed_output

-bed

boolean_true