Hi all,
reading carefully the documentation of VarScan CNA pipeline I noticed in step 4 the following suggestion:

> If all of the data and segments are consistently above or below the
> neutral value (0.0), you can re-center the data points with VarScan
> copyCaller.

My data seem to belong in this category after plotting in R using DNAcopy package. All are consistently below 0.0.
So, my question is how should I know how much I do need to re-center my data?
I mean I can calculate this by eye, but how accurate can be that?
Is there any proper way to calculate that?

Thank you in advance.

Here's an old script I have laying around that does the recentering.  Run it on the varscan copyCaller output, then repeat segmentation on the new recentered file.

https://gist.github.com/chrisamiller/f2c9e8bd565d500a8e8166fbd5eba2b1