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.
Another vote for cn.mops. I wish I had known about it when I supplied my original answer.
And another vote for cn.mops, big bonus point for me that it even works with small dataset (5-7 samples).
cn.mops performed very well for detecting CNVs in free circulating cancer DNA.
cn.mops works very well for analyzing exom sequencing data from cancer genomes
I've had great luck with CN.mops and it's relatively easy to use, even for an R newbie. Also Günter (the software's author) is very helpful and responsive!