Confusion about the cellular fraction of CNV

[ysbioinfo]

Hi I want to use the copy number information estimated by FACETS to analyze clonal evolution with PhyloWGS. In addition to some basic metrics of each segment, PhyloWGS requires another column called "cellular_prevalence". From its document files, the cellular prevalence is defined as:

Run parse_cnvs.py to create the intermediate cnvs.txt file, which will contain for each CNV its chromosome, start and end coordinates, major and minor copy numbers, and cellular prevalence (i.e., fraction of cells in sample containing the CNV, not just the fraction of tumor cells containing the CNV).

So, is the "cf" given by FACETS the same with the "cellular prevalence" required by PhyloWGS? If not, which kind of transformation should I do? I also noted that, in FACETS, the cf is 1 for normal diploid segments as there is no info about tumor. How to deal with these normal segments? Any advice will be appreciated. Yang

[veseshan]

cf is cellular fraction that contributed to the observed change i.e. cellular prevalence, For normal segments you need to figure whether PhyloWGS treats it as 0 or 1 since normal segments don't have any tumor fraction information.