Hi, I'm trying to use sciClone to infer the clonal evolution of some tumor data. I have a couple of questions about its usage (hope I'm not repeating any older question, I checked carefully but none seems satisfying):
I have vaf files (from the VarScan variant caller) containing both normal and tumor reads. Does it mean I can create 2 sciClone sample files (1 normal, 1 tumor) from them or should I just use tumor data?
What is the meaning of the five columns of the exclude regions file? (I can guess the first three are chromosome, start and end position, not quite sure about the other two)
To create the exclude regions file, I can use copy number data from the ICGC releases, where each variant (row) in the file is annotated as "copy neutral LOH", "gain" or "loss". I'm guessing I can populate the exclude regions file with all the rows in the file that are annotated as "copy neutral LOH", is it correct?
I apologize if I'm asking silly questions, I have not much experience in bioinformatics.