Hi, I want to ask whether we can estimate the copy number of the sex chromosome. Like QDNAseq, many existing tools choose to ignore the sex chromosome; however, I really need this. Normalization for copy number estimation has pre-hypothesis for diploid; however, sex chromosomes are not. Are there other ways to solve this problem? Thank you!
applyfilter(chromosomes=NA), but the result for the Y chromosome is not desirable.