Hi,
I have spent some days playing around with XHMM, and I have managed to follow and reproduce the output in the tutorial. However, I am still not sure whether XHMM is the right tool for my task at hand. It calls CNVs in all provided samples, but what I would really like is something like this:
1) Train XHMM on a large set of germline exomes to get a kind of "background" depth spectrum.
2) Take a new (cancer) sample and compare it to the background in the first step.
I would like to do (1) only once and then repeat (2) for multiple samples. When I run the example plot script, it makes plots for ALL samples, but I really just want to do it for the single sample in (2). I have tried hard to find hints in the documentation of the xhmmScripts R package, but I find it quite hard to parse.
Thanks,
Michael Knudsen