Possible problems:  - Do you have readcounts for each site in both tumors? The first two columns of the lists of variants that you feed in should be identical. - Is your tumor polyploid, or mostly CN altered? If so, no points will be usable. - Is your CN data formatted incorrectly? By default, sciClone expects absolute copy number values (CN 2 = neutral, CN 3 = 1 copy amplified, etc). You can feed it log2 values by passing the appropriate flag. - Is your data low-coverage, such that no points are exceeding the minimum depth threshold? - Chris Miller