What is the convention for a CNV caller that produces vcf output in assigning copy number to the sex chromosomes?
If there is only one copy of chrX and one copy of chrY, is the caller supposed to produce two entries with CN=1 for each of them? Or no entries?
A human male sample (hemizygous), has no extra chromosomal copies: should the CNV vcf file be empty, as there are no copy changes from the normal? Should it contain CN=1 for chrX and CN=1 for chrY?
A human sample with XXY: should the CNV vcf file report CN=2 for chrX? How is this annotation distinguished from a non-aberrant chrX CN=2?