I have WES data for 3-time points - germline, diagnosis, and relapse. I can call "somatic" mutations between germline & diagnosis and diagnosis & relapse, that will enable me to do two time-point analysis using sciClone and clonEvol. However, I can call just SNPs in each of these time points and do a sciClone+clonEvol analysis, which will not be based on somatic mutations, yet it will give me cellular clones. I can then superimpose somatic mutations on these clones. Is this a right way to do analysis since I have only three time-points? Any help will be much appreciated. Thanks!