I need to find the subclonality information of a cancer cell line exome data. For this purpose I am using sciClone. From previous threads I came to know that this tool can work with VAF information only (without providing the copy number information). However in the intermediate file created during the workflow, I can see it has assigned '
copy number 2' to every variant. I would like to know
- based on which information it has assigned value 2 as copy number to every variant?
- Is it a good idea to find subclonality information with the novel variants (after removing all the variants from public databases viz. dbSNP, 1KG, COSMIC) of a cell line?