Questions about de novo signature and parameter setting in SigProfiler #287
Description
Hi,
SigProfiler has been extremely helpful for my work, but I have some questions regarding parameter settings and de novo signature extraction.
When exome=True is set, mutations are filtered based on the predefined exome regions, which reduces the number of mutations.When I extracted mutational signatures using TCGA-CRC WES data, a new signature—SBS96D—was identified during the ASSIGNMENT stage. This signature did not appear when exome=False was set. Upon observation, I found that some of the mutational contexts of this signature are zero (e.g., C[C>A]T), and it accounts for a relatively high contribution in the samples where it is present (relevant details can be found in the figures and TXT file below).
Currently, this signature cannot be decomposed into known COSMIC signatures. I wonder if this is related to the exome parameter? Why does this situation occur? And why are some mutational contexts zero?
Looking forward to your reply! Thanks a lot.
