Description

Streams a BAM file into bedtools bamToBed with samtools (with optional filtering), then sorts the resulting BED file using GNU sort.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

bam (file)

BAM file to convert to BED format.

*.bam

Output

Name
Description
Pattern

sorted_bed

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.bed (file)

Sorted BED file generated from the input BAM.

versions_bedtools

${task.process} (string)

The name of the process

bedtools (string)

The name of the tool

bedtools --version | sed -e "s/bedtools v//g" (eval)

The expression to obtain the version of the tool

versions_samtools

${task.process} (string)

The name of the process

samtools (string)

The name of the tool

samtools version | sed "1!d;s/.* //" (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

bedtools (string)

The name of the tool

bedtools --version | sed -e "s/bedtools v//g" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

samtools (string)

The name of the tool

samtools version | sed "1!d;s/.* //" (eval)

The expression to obtain the version of the tool

Tools

samtools Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT

bedtools Documentation

BEDTools is an extensive suite of utilities for comparing genomic features in BED format.

doi: 10.1093/bioinformatics/btr539License: GPL v2.0
Pipelines with this module
genomeassembly
Authors