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Mixed PoN (Blood + FFPE) ?
I have some FFPE WGS data. I am able to access TCGA bam file. I want to build a PoN for mutation and CNA analysis with 900+ blood tissues (TCGA) and 30+ FFPE tissues (TCGA + my own). Does this PoN make sense? Many thanks!
Or, simply, which is better?
1. Only 900+ blood tissues
2. Only 30+ FFPE tissues
3. Mixed PoN