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!
The best thing here would be to not consider the germline sample as a timepoint. You have essentially two tumor timepoints: diagnosis and relapse.
So first identify the somatic variants in the diagnosis sample (relative to germline).
Next identify the somatic variants in the relapse sample (relative to germline).
Then plot the somatic variant VAFs in the diagnosis sample on one axis, and the somatic variant VAFs in the relapse sample on the other axis. This is called a 2d comparison plot here: https://github.com/genome/sciclone