cnvnator [-genome name] -root out.root [-chrom name1 ...] -tree [file1.bam ...]
Chromosome names must be specified the same way as they are described in sam/bam header, e.g., chrX or X. One can specify multiple chromosomes separated by space. If no chromosome is specified, read mapping is extracted for all chromosomes in sam/bam file. Note that this would require machines with a large physical memory of 7Gb. Extracting read mapping for subsets of chromosomes is a way around this issue. Also note that the root file is not being overwritten. To have correct q0 field for CNV calls (see below), one needs to use the option -unique when extracting read mapping from bam/sam files.
Example:
for bam files with a header like this:
or
for bam files with a header like this:
Example:
is equivalent to