Copy number analysis tool

[ni16]

Looking for efficient copy number analysis tool. I would generate data on ~100 target genes only. I am expecting significant copy number alteration in ~10 genes out of these 100. Any suggestion on the capture probe design... like whether I have to keep longer flanking sequence etc. Interestingly, I would analyse highly mixed samples and expected to have copy number alteration only in 10% of source material. Any views, what should be my take to reliably capture those copy number


Thanks