Referring to the BWA MEM docs for posterity: http://bio-bwa.sourceforge.net/bwa.shtml

Yes, secondary alignments created with -a and marked as such with -M will be handled appropriately by CNVkit, i.e. excluded from the read depth count. CNVkit calculates depth using pysam, which uses htslib internally, and will therefore handle alignments and pileups the same way as other standard-compliant tools like samtools and bwa.

Thx. May I also run BWA without any option ? (i.e. would it work to detect CNV by off-target reads ? or -a is required ? )