how to choose sequencing depth for FFPE and cfDNA tumor sample for MuTect2 ?
I am doing target panel sequencing for tumor research . now I have the following questions.
for FFPE tumor sample , what's sequencing depth is suifable for M2 calling ？
and for cfDNA tumor sample ?
and for tissue ?
if normal sample is cell type , so how sequencing depth is suitable for M2 ?
maybe I should consider 'average depth within target region ' but 'sequencing depth ' ??
I do not know how to choose suitable tumor depth and normal depth to use M2