I am Daniel Castillo Secilla, from University of Granada (Spain). I am using cn.mops for detecting CNVs but I have a question about how the paremeters WL (Windows Lentgh) works. When I used samples from the reference human genome hg19 I used a WL very low (5000) because I was trying different sizes, and the resultant plot was right, but then, I tried the same with samples from the current reference genome hg38 and, with this WL the plot has a lot of artifacts as you can see in grch38 with Artifacts image in the link below. So, I setted the WL with the value by default again (25000) and the artifacts of the plot were removed as you can see at figure grch38 without Artifacts image in the link below.
So I don't understand why these artifacts appear when the WL is too small and I hope that you can bring me some light in this situation.
grch38 with Artifacts --> https://ibb.co/fJpf4o
grch38 without Artifacts --> https://ibb.co/bA1bRd
I am looking forward to hearing from you.