"TOKENS_PON" is for WGS?
I want to analyze somation mutations in my own WGS data using Firecloud. I am a little bit confused about the ”TOKENS_PON” (as shown in the following) for Mutect filter. Based on “broad-mutation-calling-best-practice-workflows”, this PoNs comprise approximately 1000 carefully curated TCGA normals sequenced with Agilent. So, I just want to know whether this PoN includes whole genome regions and can be used in WGS mutect filtering. Since I have dbGAP account, is it better to build my own WGS PoN by TCGA blood normal sample for mutect filter? All suggestions are welcome.
Thank you very much!