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High residual variance in copy number alteration analysis

I am doing a copy number alteration analysis on liquid biopsies. After using Varscan2 and the R package DNAcopy, I got two very different types of results: Green and black distinction is made to separate different chromosomes, and the red lines are the segmentation produced by DNAcopy

On the left I got what I think it's a clean and clear result, whereas on the right I got a very "dirty" and "noisy" plot, with also a very high residual variance.

Are these samples worth keeping in the analysis? I am fairly new in this kind of analysis, but it is hard for me to trust something like what I got on the right. I was planning to remove those with high residual variance in order to keep the more stable ones, but I am not sure if this is a good practice.

Has any of you experienced something similar? How did you face this issue?

Thank you very much for your time and help!

exome copy number residual variance segmentation
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written by rmateos.1 • rmateos.1

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