Locate and tag duplicate reads in a BAM file
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM/CRAM file
*.{bam,cram}
*.bam
BAM file with duplicate reads marked/removed
*.{bam}
metrics
*.metrics.txt
Duplicate metrics file generated by biobambam
*.{metrics.txt}
versions_biobambam
${task.process}
:string
The name of the process
biobambam
The name of the tool
bammarkduplicates2 --version |& sed '1!d; s/.*version //; s/.\$//'
:eval
The expression to obtain the version of the tool
versions
biobambam is a set of tools for early stage alignment file processing.
