I have performed targeted amplicon sequencing for paired normal-tumor samples and recently identified both somatic mutations (VarScan2 somatic) and copynumber changes (CNVkit's batch command) in my samples. I would like to move on and study the tumour heterogeneity within my samples with PyClone.
Manual of CNVkit describes how data is exported into THetA2. However, as a beginner I find the manual little bit hard-to-read especially what comes to heterogeneity analysis and I can't figure out how I should run the program to obtain the input file for PyClone. Based on previous posts I know that some people have had good results with CNVkit+PyClone. I would like to see similar example script for the use with PyClone as well. Could anyone provide an example?
Thank you in advance!