Do you know of any CNV detection tools for NGS paired-end exome data - coverage method (window based) or paired-end mapping method (clustering based)? I am aware its a tough problem to solve and have looked at some tools for whole genome but couldn't find one for exome.
I would also welcome discussion about how existing tool could be re-purposed for exome through post-processing (like ignoring exon boundaries).
Finally, please feel free to point out tools for structural variants (inversions, translocations etc.) too.