I'm using the tool Control-FREEC to evaluate the CNVs in my data, but I have some doubts about the _ratio.txt file in output.
As far as I understood by both the paper and the documentation, this file should report the ratio (that, if I'm correct, should be the nr. of reads count from the sample over the nr. of reads count from the control - and not the log2 ratio) for each window, and the related estimated absolute CNs.
Currently, ratios values seem to make sense for my data, given ploidy 2 ( ratio ~1 corresponds to cn of 2, ~0.5 to 1 and so on), buth then for some windows I have ratio equal to -1. How is it possible? What does it mean?
Thank you for any answer.