I have been using VarScan to call CNV for a while but have not got a chance to look into it carefully.
The workflow basically like this: 1) Run copynumber to compare read depth between normal and tumor and get small fragments based on ration of NT/NT 2) Run circular binary segmentation (CBS) and some how merge small fragments into larger fragments again based on ration of NT/NT 3) Run mergeSegements.pl to further merge fragments and this is the final result of your CNV
I seem to understand the purpose of 1). It generate some intervals and assign each with the mean depth. These intervals are somehow like individual data point for further analysis.
What I don't understand are 2) and 3). Why do we need 2 steps of merging? What is the difference of these 2 steps? Why can't we just merge once and achieve the purpose? Why can't we set up more appropriate criteria / perimeters at the very first step (step 1) and spare the merging step?