I'm using CNVkit to detect copy number changes in my samples which have been obtained from amplicon sequencing (sequenced region is around 330kb). I have 8 normal samples and 20 test samples. I can detect the copy number regions in the test samples, however how do I find out the copy number changes in the normal samples?
I created a reference CNN using the normals and reference genome (hg19). The CNN file generated does show the chr,start,end, log2, among other things. Can I use the log2 value to determine the copy number regions in the normal samples, or is there any other way to find out that information?
Any help appreciated!