bedtools/bedtools_bamtobed

Converts

BAM

BED

BED6

BEDPE

Description

Converts BAM alignments to BED6 or BEDPE format.

Type

bash_script

License

MIT

Keywords

Converts

BAM

BED

BED6

BEDPE

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"  
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_bamtobed/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input BAM file.

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output BED file.

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--bedpe	boolean_true	Write BEDPE format. Requires BAM to be grouped or sorted by query.
--mate1	boolean_true	When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE "block".
--bed12	boolean_true	Write "blocked" BED format (aka "BED12"). Forces -split. See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
--split	boolean_true	Report "split" BAM alignments as separate BED entries. Splits only on N CIGAR operations.
--splitD	boolean_true	Split alignments based on N and D CIGAR operators. Forces -split.
--edit_distance -ed	boolean_true	Use BAM edit distance (NM tag) for BED score. - Default for BED is to use mapping quality. - Default for BEDPE is to use the minimum of the two mapping qualities for the pair. - When -ed is used with -bedpe, the total edit distance from the two mates is reported.
--tag	string	Use other NUMERIC BAM alignment tag for BED score. Default for BED is to use mapping quality. Disallowed with BEDPE output.
--color	string	An R,G,B string for the color used with BED12 format. Default is (255,0,0).
--cigar	boolean_true	Add the CIGAR string to the BED entry as a 7th column.

Name

Type & Properties

--bedpe

boolean_true

--mate1

boolean_true

--bed12

boolean_true

--split

boolean_true

--splitD

boolean_true

--edit_distance

-ed

boolean_true

--tag

string

--color

string

--cigar

boolean_true