CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.
meta
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
bam
:file
Sorted BAM/CRAM/SAM file
*.bam
bai
meta2
root
ROOT file
*.root
meta3
Groovy Map containing reference information e.g. [ id:'test' ]
[ id:'test' ]
fasta
Path to a directory containing fasta files or a fasta file
*.fa
meta4
fai
Path to a fasta file index
*.fai
step
:string
One of “his”, “rd”, “call”, “stat”, and “partition”
output_meta
${prefix}.root
A ROOT file
tab
${prefix}.tab
A tab file containing cnvnator calls
*.tab
versions_cnvnator
${task.process}
The name of the process
cnvnator
The name of the tool
cnvnator 2>&1 | sed -n '3s/CNVnator v//p'
:eval
The expression to obtain the version of the tool
versions
Tool for calling copy number variations.
