bedtools/bedtools_bedtobam

Converts

BED

GFF

VCF

BAM

Description

Converts feature records to BAM format.

Converts genomic intervals from BED, GFF, or VCF formats into BAM format,
creating aligned sequence records that can be used with standard BAM tools.

Type

bash_script

License

MIT

Keywords

Converts

BED

GFF

VCF

BAM

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"  
map_quality: [ 255 ]  
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_bedtobam/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input genomic intervals file in BED, GFF, or VCF format. Requirements: - BED files must be at least BED4 format (requires name field) - File must contain valid genomic coordinates
--genome -g	file required	Genome file defining chromosome names and sizes. Format: Two-column tab-delimited file: ``` chr1 249250621 chr2 243199373 ``` Note: This is NOT a FASTA file. Use `samtools faidx` to create from FASTA if needed.

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output BAM file containing converted genomic intervals. Format: Standard BAM format (compressed by default)

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--map_quality -mapq	integer	Set the mapping quality for the BAM records. Range: 0-255 (higher values indicate better quality) Default: 255 (maximum quality)
--bed12	boolean_true	Process BED file as BED12 format with blocked intervals. Features: - BAM CIGAR string reflects BED blocks (exons/introns) - Useful for representing spliced alignments - Requires BED12 format input
--uncompress_bam -ubam	boolean_true	Write uncompressed BAM output. Default behavior: Writes compressed BAM Use case: When downstream tools require uncompressed format

Name

Type & Properties

--map_quality

-mapq

integer

--bed12

boolean_true

--uncompress_bam

-ubam

boolean_true