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.

Type

bash_script

License

MIT

Keywords

genomics

intervals

format conversion

BAM

BEDPE

paired-end

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.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

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

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

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.

Name

Type & Properties

--output

file

required

output

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

Name

Type & Properties

--mapq

integer

--ubam

boolean_true