Hi, I have been using CNVkit for 3 months now and discovering few interesting things.
These are my questions: 1) How can plot copy number segments of paired tumor and normal samples on the same scatter plot? Something like this
2) I have done Segmentation and Segment Calling. Applied the default threshold values (-t=-1.1,-0.4,0.3,0.7) at the 'Call' step. But the number of Copy number positions did not change with the applied threshold. For example, My .segments.cns file had 100 CNV positions with the applied threshold, there should be a decrease in the number. But that didn't happen!! Am I doing something wrong??
3) How can use -t (threshold) at segmentation step? Does it need 4 threshold values like the call step?
I'd really appreciate if someone could answer my questions.