Dear all,

I need to get major and minor cn values on some TSO500 tumor samples and one pooled Normal sample to calculate ccf, thus, I am running cnvkit in non-batch mode for copy number evaluation. In the output of cnvkit call there is no baf or cn1/2 columns when I use Tumor vcf files. and here is the command using Tumor samples:

cnvkit.py call input.cns -v input.vcf -o output.call.cns 

Would you please help me how to solve these issues.

Many thanks in advance, Rahel