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
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) |
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 |
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 |
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 |
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 |
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 |
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 v0.4.1 \
-main-script target/nextflow/bedtools/bedtools_pairtobed/main.nf \
-params-file params.yaml Relationships
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Current component
bedtools/bedtools_pairtobedbiobox v0.4.1
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