bedtools/bedtools_bedtobam

Converts

BED

GFF

VCF

BAM

Description

Converts feature records (bed/gff/vcf) to BAM format.

Type

bash_script

License

MIT

Keywords

Converts

BED

GFF

VCF

BAM

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
map_quality: [ 255 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/bedtools/bedtools_bedtobam/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file (bed/gff/vcf).
--genome -g	file required	Input genome file. NOTE: This is not a fasta file. This is a two-column tab-delimited file where the first column is the chromosome name and the second their sizes.

Name

Type & Properties

--input

-i

file

required

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output -o	file output	Output BAM file to be written.

Name

Type & Properties

--output

-o

file

output

Options

Name	Type & Properties	Description
--map_quality -mapq	integer	Set the mappinq quality for the BAM records.
--bed12	boolean_true	The BED file is in BED12 format. The BAM CIGAR string will reflect BED "blocks".
--uncompress_bam -ubam	boolean_true	Write uncompressed BAM output. Default writes compressed BAM.

Name

Type & Properties

--map_quality

-mapq

integer

--bed12

boolean_true

--uncompress_bam

-ubam

boolean_true