I am using phylowgs on longitudinal tumor samples ie. before after treatment. I had read (somewhere in the issues or readme) that vaf distributions reported for multi-sample run would be a summary of all samples used in the run, and therefore should not be used. Is it also true for LI,BI,CCI? I am looking for a complexity parameter that I can use. If they are sums, should I be running samples separately and compare the indices such as before/after to see how they evolve? Or is it possible that this information lies somewhere in the multi-sample run results?
Hi,
I am using phylowgs on longitudinal tumor samples ie. before after treatment. I had read (somewhere in the issues or readme) that vaf distributions reported for multi-sample run would be a summary of all samples used in the run, and therefore should not be used. Is it also true for LI,BI,CCI? I am looking for a complexity parameter that I can use. If they are sums, should I be running samples separately and compare the indices such as before/after to see how they evolve? Or is it possible that this information lies somewhere in the multi-sample run results?
Thanks a lot for your help and this great tool,
Irem