Impact of FFPE preservation

[mybabyfox]

Hi all,

I wonder if anyone can share your experience with Facets analysis result on FFPE samples. Specifically, I am curious if FFPE preservation can lead to potential noises(e.g., potential false amplifications/deletions) in the result.

Meanwhile, I wonder if there are parameters in the BAM preprocess or normalization steps that we can fine tune to tackle FFPE's impact.

Thank you all.