We're performing NGS on cancer DNA samples with a custom panel of target regions in different genes.
From your experience & knowledge, which tools do you recommend using for our purpose:
1. Finding structural variants (SVs) such as inversions, large indels, translocations, tandem duplications, etc.
2. CNV (copy number variantion) discovery for only a single sample (many tools I've found were for multiple samples).
If i'm not mistaken I should look for tools that are suitable for exome data rather than whole genome because of our sequencing methods and custom panel.
Thank you very much in advance!
I realize this has been somewhat asked before but the posts I've found were at least 2-3 years old and didn't elaborate on cancer genomics or exome sequencing. It was also unclear to me which CNV discovery tools are suitable for single samples. I hope this isn't out of line.