What are currently the best copy number variantion calling tools?
Is there a distinction between the best tools suited for whole genome or exome data? Or are the tools that claim to be good at CNV calling for exome data (for instance Varscan) also well suited for CNV calling in whole genome data?
Are there more of these distinctions between CNV caller tools?
Next to exome - whole genome another important difference between the tools is that some require matched case-control samples (like CNV-seq) and some do not (like ControlFreec). While you are waiting for a better answer/comment this list of CNV tools for NGS sequencing might be worth looking at.
Apparently, ControlFreec DOES handle the matched case-control. From the second paragraph of the link you provided : "The control (matched normal) sample is optional."
Sorry, meant require, changed it
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
There is a huge difference between germline CNVs and somatic CNAs calling.