I have 60 BAM files corresponding to 60 different individual strains. To do CNV calling on this dataset, should I read all the files together in parallel, or work on each strain individually, merge the root files, and continue analysis. The README is a little unclear because the step to extract read mapping seems to indicate you can provide multiple BAMs at once: ./cnvnator [-genome name] -root out.root [-chrom name1 ...] -tree [file1.bam ...]

Yet later on it suggests merging together root files before CNV calling: ./cnvnator [-genome name]-root out.root [-chrom name ...] -merge file1.root ...

Is there a difference between these two? Is one method favored over the other?

EDIT: corrected second line of code copied from README