In reading through the documentation of tools like Illumina Manta, DNAnexus Parliament, Delly, Mobster - they make reference to CNV as one of the types of structural variation that can be detected.

However, when I read through CNVkit's documentation it is extremely thorough and specific to amplifications and deletions.

How do these more general SV tools compare to CNVkit? Our use case is "moving beyond SNP/LD-based GWAS" into CNV.