Dealing with C>T technical issues (from FFPE samples) in SNP analysis

Question

[dodausp]

Hi all, I have always wondered why C>T transitions are frequently high when performing SNP analysis, and even more evident when looking for somatic signatures. I have only worked with FFPE samples, so it never crossed mind that the fixation procedure might be the problem, until I found this (Do et al, 2013):

...we also observed that C:G>
T:A SNCs often accounted for
50% of all artifactual SNCs in FFPE DNA samples.

That explains a lot!

So, considering this alarmingly high rate of artifacts, I believe that people account for that error and somehow filter them out. That being said, is there any procedure/script/package to overcome this issue?

Any help is much appreciated!