I'm relatively new to CNV analysis. I ran cnvkit on WGS samples (4 tumor/normals) and the normals were pooled.
I don't quite understand how the log2 values in .cnr files for CNVkit are calculated.
Here is a result from one of my sample:
chr1 11129 12259 DDX11L1 28.2027 4.81772
chr1 11129 12259 DDX11L1 373.432 8.54083
chr1 11129 12259 DDX11L1 373.432 -0.23305 0.805129
As can be seen from .cnn files, the tumor has higher depth, but in .cnr file it has negative log ratio. I looked at other normal samples in the same region and they almost have similar depth and log values in their .cnn file.
So, why is it the log ratio .cnr file for this bin negative?
Thanks for the help!