Description

Parallel sorting and duplicate marking

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bams (file)

List containing 1 or more bam files

meta2 (map)

Groovy Map containing genome information
e.g. [ id:‘genome’ ]

fasta (file)

Reference genome in FASTA format (optional)

*.{fa,fasta,fna}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file with duplicate reads marked/removed

*.bam

bam_index (file)

BAM index file

*.bai

cram (file)

CRAM file with duplicate reads marked/removed

*.cram

metrics (file)

Duplicate metrics file generated by biobambam

*.{metrics.txt}

versions (file)

File containing software versions

versions.yml

Tools

biobambam
GPL v3

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