I need to perform GISTIC and MutSig analyses on a cohort of samples. Some of these samples have multiple biopsies taken at both A) same time point, B) different time points. I was wondering what the best way is to go about this situation for the two analyses I mentioned:
1) For MutSig, how would it affect the results if I took the union of all mutation calls from the different tissues per patient?
2) For GISTIC, is it even possible to take a "union" of the copy number calls?
3) Again for GISTIC, is it advisable to take an average of the copy number calls across all the samples per patient?
I wanted to know if there is a best practice to deal with such situations while performing the said analyses. Thanks!