I have some high coverage exome data for my normal/tumor pairs where I am particularly interested in calling the CNV/ I am also having reprogrammed clones from the tumor to give IPSC(induced pluripotent stem cells). I am now trying to understand by CNV calling by the Control-FREEC method how the loss or gain in copy is conserved across tumor and its IPSC, does the genetic background is entirely wiped out still it is conserved and shows potential oncogenes. I have found some hits infact. The thing which bothers me is in Control-FREEC there is no option to give find how significant are the CNV calls, like you get an output file with .CNV which is having the coordinates with the copies gained or lost for each chromosomes but how can we select which should be the true positives. I have 90 CNVs called for my tumor and around 200 for my IPSC, out of them barely 50% coincides with the known CNVs when I tried to merge them with the CNV database making them TP but then rest can either be FP or novel as well. Is there any way to judge that with CNV calls from Control-FREEC. The software is excellent with good visualization plot but I am confused in this part . Would be happy if someone shares some ideas. Also I would like to know is it possible to have 8 or 9 copies for a region on the chr , the same has been mimicked in my IPSC as well for the exact region but is it feasible to have such high copy number ? I would be grateful if someone can share some light.