As airan mentioned, CNVnator is useful for some genomes (it was mainly designed for human/mouse IIRC). However, the genome you are aligning against, and in particular the difference in your sample vs that reference and how much of the genome is repetitive, makes a huge difference in what you should run.

For instance, CNVnator gave fairly terrible results on a plant genome we did recently, for both of the reasons above. The genome was ~80% repetitive and quite different than the reference. We ended up essentially getting much more information, and much less noise, by simply generating read coverage stats from genic regions and assessing those directly for gain/loss.