Please see the attached. I try to understand why Tumour 1 has most of the copy number equal to 1, but most of my past analyses (e.g. sequenza) and other works have most in the copy number =2 (same as Normal). Could you give me an insight of this interpretation?
I ran: 1.cnvkit.py batch 2.cnvkit.py export theta Sample_Tumor.cns Sample_Normal.cnr -o Sample.theta2.input 3./path/to/theta2/bin/RunTHetA Sample.theta2.input
Note I ran THeTA2 to get tumour purity and number of subclones. Is it something due to that "CNVkit only reports the estimated log2 copy ratio, and does not currently attempt a formal statistical test for estimating integer copy number"?