Excuse me, I hope someone can tell me how to prepare the input for Pyclone.
Now I have the WES data of a dysplasia and a tumor sample, I want to explore the subclonal structures between the two. In my opinion, I think the input for Pyclone should be the union of mutations from the two samples. For example, mutation A is in the dysplasia MAF file, and mutation B is in the tumor MAF file. In order to make the input, I have to know the ref_counts and var_counts of mutation union in every sample. But from my MAF files, I can only know the ref_counts and var_counts of mutation A in the dysplasia MAF file, I don't know the counts of mutation A in the tumor MAF file, so how can I solve this problem?
Thank you very much in advance！
Excuse me, I hope someone can tell me how to prepare the input for Pyclone. Now I have the WES data of a dysplasia and a tumor sample, I want to explore the subclonal structures between the two. In my opinion, I think the input for Pyclone should be the union of mutations from the two samples. For example, mutation A is in the dysplasia MAF file, and mutation B is in the tumor MAF file. In order to make the input, I have to know the ref_counts and var_counts of mutation union in every sample. But from my MAF files, I can only know the ref_counts and var_counts of mutation A in the dysplasia MAF file, I don't know the counts of mutation A in the tumor MAF file, so how can I solve this problem? Thank you very much in advance！