Hi, I have tried to use cnvkit to detect copynumbers in circulating tumor DNA samples. I used the "batch -m amplicon" command with both cancer and normal samples followed by "call" to get absolute copy numbers. The results doesn't correlate much with the "actual" copyumbers in my data (I also have whole genome samples of the same patients to compare with). I get a lot of false CN calls of 0 and some really high, like 35 (that should be 2)
So my question is that is there any additional steps to batch and call that I could use to get better results? And is there anyone that has experience using cnvkit for ctDNA samples?