why genomewide CNV is not so "normalized" as in reference

[asaki1986]

Hi,

I am using ichorCNA to process the 1x WGS data for miscarriage samples. Using data from normal samples as reference, we tend to estimate the CNV status of the genome. We found the genomewide CNV plot is very noisy against the reference, which is largely different from the plot presented in reference.

Any method to get the plot more smoothly?

Thanks, Junfeng

[asaki1986]

Any method to make the data normalized?