bedtools/bedtools_pairtobed

genomics

paired-end

bedpe

overlaps

structural-variants

bam

intervals

Description

Report overlaps between a BEDPE file and a BED/GFF/VCF file.

bedtools pairtobed finds overlaps between paired-end intervals (BEDPE format)
and genomic features in BED/GFF/VCF format. This tool is particularly useful
for analyzing paired-end sequencing data, structural variants, or any genomic
data where you need to consider relationships between paired intervals.

This tool is commonly used for:

Annotating structural variants with genomic features
Finding overlaps between paired-end ChIP-seq reads and genes
Analyzing chromatin interactions (Hi-C, ChIA-PET) with genomic annotations
Quality control of paired-end sequencing experiments
Intersecting BEDPE format data with reference annotations
Processing BAM files with paired-end alignment information

Type

bash_script

License

MIT

Keywords

genomics

paired-end

bedpe

overlaps

structural-variants

bam

intervals

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: [ "either" ]  
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_pairtobed/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--bedpe -a	file required	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: Pairs will be tested for overlaps with features in --bed file Requirements: Must be in valid BEDPE format
--bed -b	file required	Input BED/GFF/VCF file with genomic features. Format: BED, GFF, or VCF file with genomic coordinates Content: Genomic features to test for overlaps with BEDPE pairs Usage: Features will be intersected with paired intervals from --bedpe Requirements: Standard genomic coordinate format
--bam_input -abam	file	Input BAM file instead of BEDPE file. Format: BAM format with paired-end alignments Content: Paired-end sequencing reads Requirements: Must be grouped or sorted by query name Usage: Replaces --bedpe argument when working with BAM input Output: Will produce BAM output by default (unless --bedpe_output is used)

Name

Type & Properties

--bedpe

-a

file

required

--bed

-b

file

required

--bam_input

-abam

file

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with overlap results. Format: Depends on input type and options BAM input: BAM format (unless --bedpe_output specified) BEDPE input: BEDPE format with overlapping pairs Content: Original paired intervals that meet the overlap criteria

Name

Type & Properties

--output

file

required

output

Output Options

Name	Type & Properties	Description
--uncompressed_bam -ubam	boolean_true	Write uncompressed BAM output. Usage: Only applies when using BAM input (--bam_input) Default: Compressed BAM output Effect: Produces larger but faster-to-write output files Applications: When downstream tools require uncompressed BAM
--bedpe_output -bedpe	boolean_true	Write output in BEDPE format when using BAM input. Usage: Only applies when using BAM input (--bam_input) Default: BAM output when BAM input is used Effect: Converts BAM pairs to BEDPE format in output Applications: When you need text-based output from BAM input

Name

Type & Properties

--uncompressed_bam

-ubam

boolean_true

--bedpe_output

-bedpe

boolean_true

Overlap Options

Name	Type & Properties	Description
--min_overlap -f	double	Minimum overlap required as fraction of BEDPE intervals. Default: 1E-9 (effectively 1 base pair) Range: 0.0 to 1.0 Usage: Overlap must be at least this fraction of the BEDPE interval Example: 0.5 requires 50% overlap
--type	string	Approach for reporting overlaps between BEDPE and BED. either: Report if either end of BEDPE overlaps BED (default) neither: Report if neither end of BEDPE overlaps BED both: Report if both ends of BEDPE overlap BED xor: Report if exactly one end of BEDPE overlaps BED notboth: Report if neither or exactly one end overlaps (xor + neither) ispan: Report overlaps between [end1, start2] span of BEDPE and BED ospan: Report overlaps between [start1, end2] span of BEDPE and BED notispan: Report if ispan doesn't overlap BED notospan: Report if ospan doesn't overlap BED

Name

Type & Properties

--min_overlap

-f

double

--type

string

Strand Options

Name	Type & Properties	Description
--same_strand -s	boolean_true	Require same strandedness when finding overlaps. Default: Ignore strand information Usage: Only report overlaps on the same strand Note: Not applicable with ispan, ospan, notispan, or notospan types Applications: Strand-specific analyses
--opposite_strand -S	boolean_true	Require different strandedness when finding overlaps. Default: Ignore strand information Usage: Only report overlaps on opposite strands Note: Not applicable with ispan, ospan, notispan, or notospan types Applications: Antisense interaction analyses

Name

Type & Properties

--same_strand

-s

boolean_true

--opposite_strand

-S

boolean_true

BAM-specific Options

Name	Type & Properties	Description
--edit_distance -ed	boolean_true	Use BAM total edit distance (NM tag) for BEDPE score. Default: Use minimum mapping quality of the two mates as score Usage: Only applies when using BAM input (--bam_input) Effect: Reports total edit distance from both mates as the score Applications: Quality assessment based on sequence accuracy

Name

Type & Properties

--edit_distance

-ed

boolean_true