I'm planing to use CNVnator to call CNVs but my sample has 4 bam files of 20Gb each, where chromosome are not sorted. So in total that's 80GIGABytes (Yes I said GIGA Bytes haha).

Can I query CNVs on all chromosome in one shot or do I have to do that by batch of chromosomes.. ?

So if I do the following for every chromosome at a time is it going to work efficiently?

./cnvnator -root NA12878.root -chrom chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chr23  -tree myfile1.bam myfile2.bam myfile3.bam myfile4.bam