bedtools/bedtools_bedpetobam
genomics
intervals
format conversion
BAM
BEDPE
paired-end
Description
Convert BEDPE (paired-end BED) intervals to BAM format.
This tool converts genomic paired-end interval data into BAM alignment format,
where each BEDPE record becomes a pair of BAM alignment records representing
the paired-end reads.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file in BEDPE format. **BEDPE format:** Tab-delimited with 10 columns: chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2 **Requirements:** Represents paired-end genomic intervals **Coordinate system:** 0-based coordinates |
--genome -g | file required | Genome file defining chromosome names and sizes. **Format:** Tab-delimited file with chromosome name and size **Example line:** chr1 249250621 **Purpose:** Required for BAM header creation |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output BAM file. Contains converted BEDPE intervals as paired BAM alignment records suitable for visualization and downstream analysis of paired-end data. |
BAM Options
Name | Type & Properties | Description |
|---|---|---|
--mapq | integer | Set the mapping quality for BAM records. **Range:** 0-255 (typical values) **Default:** 255 (maximum quality) **Purpose:** MAPQ field in BAM format |
--ubam | boolean_true | Write uncompressed BAM output. **Default:** Compressed BAM output **Use case:** When compression is not needed or causes issues **File size:** Significantly larger output files |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.bam"
mapq: [ 255 ]
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_bedpetobam/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
bedtools/bedtools_bedpetobambiobox v0.4.1
Uses
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