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
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 |
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 |
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 |
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 |
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 Relationships
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Current component
bedtools/bedtools_pairtopairbiobox v0.4.0
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