I'm using ExomeDepth R package for CNV analysis and I have few questions
First, I understand that the reference is chosen by the correlation between each samples, but there is also some column as 'expected.BF', 'phi' ... I don't understand how the tool choose the reference. Is there a threshold ? How can I interpreter the phi value and the expected.BF ?
Also, How is generate the final correlation (<0.97) ? In fact, in my results, the max correlation between each sample is 0.94, however I have a final correlation 0.99
To finish, from how many reads the tools considers that there is a CNV ?