Parallel sorting and duplicate marking
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bams
List containing 1 or more bam files
fasta
Reference genome in FASTA format (optional)
*.{fa,fasta}
bam
BAM/CRAM file with duplicate reads marked/removed
*.{bam,cram}
bam_index
BAM index file
*.{bai}
metrics
Duplicate metrics file generated by biobambam
*.{metrics.txt}
versions
File containing software versions
versions.yml
biobambam is a set of tools for early stage alignment file processing.
