Description

Locate and tag duplicate reads in a BAM file

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

bam:file

BAM/CRAM file

*.{bam,cram}

Output

name:type
description
pattern

bam

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.bam:file

BAM file with duplicate reads marked/removed

*.{bam}

metrics

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.metrics.txt:file

Duplicate metrics file generated by biobambam

*.{metrics.txt}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

biobambam
GPL v3

biobambam is a set of tools for early stage alignment file processing.