bedtools/bedtools_pairtopair

genomics

paired-end

bedpe

structural-variants

intersect

chromatin-interactions

Description

Report overlaps between two paired-end BED files (BEDPE).

bedtools pairtopair finds overlaps between paired-end intervals in two BEDPE files.
This tool is particularly useful for comparing structural variants, chromatin interactions,
or any paired-end genomic data between different samples or conditions.

This tool is commonly used for:

Comparing structural variants between samples
Intersecting Hi-C or ChIA-PET datasets
Finding common paired-end features across experiments
Analyzing concordance between paired-end calling methods
Quality control of structural variant detection pipelines
Cross-referencing chromatin interaction datasets

Type

bash_script

License

MIT

Keywords

genomics

paired-end

bedpe

structural-variants

intersect

chromatin-interactions

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.bedpe"  
type: [ "both" ]  
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_pairtopair/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--bedpe_a -a	file required	First input BEDPE file with paired interval data. Format: BEDPE format with paired genomic coordinates Content: Each line represents a pair of genomic intervals Columns: chrom1, start1, end1, chrom2, start2, end2, [name], [score], [strand1], [strand2] Usage: Primary dataset to find overlaps for Requirements: Must be in valid BEDPE format
--bedpe_b -b	file required	Second input BEDPE file with paired interval data. Format: BEDPE format with paired genomic coordinates Content: Each line represents a pair of genomic intervals Columns: chrom1, start1, end1, chrom2, start2, end2, [name], [score], [strand1], [strand2] Usage: Reference dataset to intersect with dataset A Requirements: Must be in valid BEDPE format

Name

Type & Properties

--bedpe_a

-a

file

required

--bedpe_b

-b

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with overlapping paired intervals from dataset A. Format: BEDPE format containing overlapping pairs from input A Content: Only pairs from dataset A that meet overlap criteria with dataset B Filtering: Results depend on overlap type and threshold parameters

Name

Type & Properties

--output

file

required

output

Overlap Options

Name	Type & Properties	Description
--min_overlap -f	double	Minimum overlap required as fraction of dataset A intervals. Default: 1E-9 (effectively 1 base pair) Range: 0.0 to 1.0 Usage: Overlap must be at least this fraction of A's interval length Example: 0.05 requires 5% overlap
--type	string	Approach for reporting overlaps between BEDPE datasets. both: Report if both ends of A overlap B (default) either: Report if either end of A overlaps B neither: Report if neither end of A overlaps B notboth: Report if one or neither end of A overlaps B Usage: Defines the overlap stringency requirement
--slop	integer	Amount of slop (in base pairs) to add to each footprint of dataset A. Default: 0 (no slop) Usage: Extends intervals before overlap detection Effect: Slop is subtracted from start1/start2 and added to end1/end2 Applications: Finding near-misses or fuzzy overlaps
--strand_slop -ss	boolean_true	Add slop based on strand information. Plus strand: Slop only added to end coordinates Minus strand: Slop only added to start coordinates Default: Slop added in both directions regardless of strand Requirements: Requires strand information in BEDPE files

Name

Type & Properties

--min_overlap

-f

double

--type

string

--slop

integer

--strand_slop

-ss

boolean_true

Filtering Options

Name	Type & Properties	Description
--ignore_strand -is	boolean_true	Ignore strand information when searching for overlaps. Default: Strand information is enforced Usage: Overlaps reported regardless of strand orientation Applications: When strand doesn't matter for the analysis
--require_different_names -rdn	boolean_true	Require overlapping pairs to have different names. Default: Same names are allowed Usage: Avoids self-hits when datasets contain overlapping entries Applications: Comparing datasets that might have common entries Effect: Filters out pairs with identical names between datasets

Name

Type & Properties

--ignore_strand

-is

boolean_true

--require_different_names

-rdn

boolean_true