I am working with DNA-seq and the cn.mops R package. Firstly, i was working with BAM files aligned with the reference genome hg19 and all work fine! But now I am working with BAM aligned with the hg38 reference genome and the plots of cn.mops are a bit different. I think that this can be due to the improvements of the hg38 in comparison with hg19 but I don't know exactly if I can use cn.mops with data from hg38 genome. How shoud I interpretate them? I attach you some photos with the resultant plots.
Thank you very much in advance.