1) Regarding the mutation lists, If you call the following mutations: Tumor 1: 1 111 10 10 50.0 2 222 9 9 50.0 Tumor 2: 1 999 8 8 50.0 2 888 7 7 50.0 You then need to merge the calls and pull readcounts for every site in both samples, so your files will look like: Tumor 1: 1 111 10 10 50.0 1 999 6 6 50.0 2 222 9 9 50.0 2 888 5 5 50.0 Tumor 2: 1 111 4 4 50.0 1 999 8 8 50.0 2 222 3 3 50.0 2 888 7 7 50.0   2) Read the sciClone paper for a full explanation of why we only consider copy-number neutral sites for clustering: http://www.ploscompbiol.org/article... - Chris Miller