Conceptually I can imagine how to do this. But, does anyone have a recommendation for a well established pipeline or tool for identifying a viral integration site in the human genome. Suppose I have 50X WGS data for a tumor sample and 30X WGS data for a normal sample and am looking for a specific virus (e.g. HBV) which is known to integrate into the genome for my cancer of interest. I want to be able to answer two simple questions: (1) Is there evidence of viral integration? (2) What is the exact breakpoint/integration site?
Any suggestions will be greatly appreciated.