I am planing to use Mutect2 to discover SNV/Indels.
I read here that the panel of normals should be crated from "from subjects that were young and healthy to minimize the chance of using as normal a sample from someone who has an undiagnosed tumor". So I obviously thought, that I cannot use my matched normals to create the PON, because these individuals obviously already have a diagnosed tumor for which I am trying to determine the SNV.
Nonetheless, I saw online in some workshops, that they did exactly that: They used the matched normal to create the PON.
I know that it is possible to run Mutect2 without a PON, so my question is, if this is "okay" to do.
To put it in another way:
Should I rather run Mutect2 without any PON if I am not able to create one, or should I in this case use my matched normal to create the PON?
Any help is much appreciated!
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