I want to ask that can we use breakerdancer, manta,delly, lumpy-sv for copy number variation calling of whole exome analysis? I have just whole exome data of five patients and I want to call their copy number variations.
I worked on CNVs detection in the recent past, and I developed a simple wrapper for a CNV simulator developed by NabaviLab that I found a little bit complicated in the first place. (WARNING : Simulation is slow!)
You can maybe simulate reads similar to you real data (similar depth of coverage, similar balancing in term of amplifications and deletions given what you expect to find, etc) with CNVs inserted in known place and then test the different tools to find which one suits better your task!