Estimate tumor contamination in normal sample
Hello again- I'd like to hear your thoughts about estimating the tumour contamination in a normal sample. (This is useful to know when the matched normal is tissue adjacent to the tumor).
From Estimate cross-sample contamination using GetPileupSummaries and CalculateContamination I see that the combination of getPileupSummaries+CalculateContamination is not appropriate for this task.
However, I see in mutect.pdf, section VII, a proposed strategy for estimating tumor in normal. Do you have any experience/recommendations about it?
Thanks a lot!