cnvnator [-genome name] -root file.root [-chrom name1 ...] -his bin_size [-d dir]
This step is not memory consuming and so can be done for all chromosomes at once. It can, of course, be carried for a subset of chromosomes also. Files with chromosome sequences are required and should reside in the running directory or in the directory specified by the -d option. Files should be named as: chr1.fa, chr2.fa, etc.