7 months ago by
The Institute of Cancer Research, London
Hi fantastycrane, the GitHub space for REVOLVER contains a wiki with some FAQ, and vignettes that you might want to look at if you decide to use the tool. Concerning your CCF-related question, to explain it shortly CCF estimates - and their clusters - are computed doing what we call "subclonal deconvolution", which requires 1) SNV 2) copy number calls, and 3) tumour purity estimation (contamination of non-tumour cells in the bulk sample). With that data there are several tools that you can use to compute the CCF values, and their clusters. Two tools that I like are pyClone and sciClone etc, for which you find support either here, or on the tool webpage.
So that bit of the analysis does not happen within REVOLVER because there are dedicated tools for it. Feel free to drop a line if you try that analysis and something does not work out for you. For questions regarding REVOLVER etc, you can also use the GitHub issue page.
REVOLVER Wiki: https://github.com/caravagn/revolver/wiki Issues: https://github.com/caravagn/revolver/issues