To find CNVs you need control samples from the same sequencing type. For example, if you have a case file sequenced by Sure Select V4 then you need control from Sure Select V4. You should rather use tools which would detect CNV without control bams. I think cn.mops detects CNVs without control bam files. But, please check before. Also, There might be control samples available on NCBI which would have undergone identical sequencing experiment to yours. Try find those samples for your controls. (Do this only if you could not find any other tool for detection of CNV).
Hi BAGeno, Contra has a baseline.py script that can create a control from your sample bams. I'm running into some errors with it at the moment but the documentation is here: http://contra-cnv.sourceforge.net/ at the end of the page.