bedtools/bedtools_bamtobed

Converts

BAM

BED

BED6

BEDPE

Description

Converts BAM alignments to BED6 or BEDPE format.

This tool converts alignments in BAM format to either BED6 or BEDPE format,
allowing for flexible downstream analysis of genomic intervals.

Inputs

Name	Type & Properties	Description
--input -i	file required	Input BAM file containing aligned sequences. Requirements: - Must be in SAM/BAM format - For paired-end BEDPE output (`--bedpe`), must be grouped or sorted by query name

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output file in BED or BEDPE format. Output formats: - Default: BED6 format (6 columns) - With `--bedpe`: BEDPE format for paired-end data - With `--bed12`: BED12 format with blocked intervals

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--bedpe	boolean_true	Write BEDPE format for paired-end data. Requirements: - BAM must be grouped or sorted by query name - Produces paired-end BED format with mate information
--mate1	boolean_true	When writing BEDPE format (`--bedpe`), always report mate one as the first BEDPE block. Ensures consistent ordering of paired-end reads in output.
--bed12	boolean_true	Write blocked BED format (BED12 format). Features: - Creates 12-column BED format with block information - Automatically forces `--split` option - Useful for representing spliced alignments See [BED12 format specification](http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1) for details.
--split	boolean_true	Report split BAM alignments as separate BED entries. Behavior: - Splits only on N CIGAR operations (introns/gaps) - Each split becomes a separate BED interval - Useful for RNA-seq data with spliced alignments
--splitD	boolean_true	Split alignments based on both N and D CIGAR operators. Features: - Splits on N (gaps/introns) and D (deletions) operations - Automatically forces `--split` option - More aggressive splitting than `--split` alone
--edit_distance -ed	boolean_true	Use BAM edit distance (NM tag) for BED score instead of mapping quality. Scoring behavior: - Default BED: Uses mapping quality as score - Default BEDPE: Uses minimum of two mapping qualities - With --ed + --bedpe: Reports total edit distance from both mates
--tag	string	Use other numeric BAM alignment tag for BED score. Usage: - Specify any numeric BAM tag (e.g., `SM`, `AS`, `XS`) - Replaces default mapping quality scoring - Not allowed with BEDPE output format
--color	string	RGB color string for BED12 format visualization. Format: R,G,B values (0-255 each) Default: `255,0,0` (red)
--cigar	boolean_true	Add the CIGAR string as a 7th column in BED output. Useful for preserving alignment information in BED format.

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

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bed"  
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_bamtobed/main.nf \  
  -params-file params.yaml

bedtools/bedtools_bamtobed

Inputs

Outputs

Options

Run this component

Relationships

Used by

Uses