For what I understand, the GATK's best practices recommends the usage of a Panel of Normals (PON) for an accurate somatic mutation detection. By having a large enough pool of "normal" samples, it is possible to detect technical biases created by the sequencing machine, the protocol, the kit, etc. Please correct me if I'm wrong.
With this said, I'd like to analyse WGS data coming from BGI, using DNBseq platform instead of the industry standard Illumina. If I do not have a set of "normal" samples sequenced in the same way as my WGS data, is it accurate to use a generic PON (even if it's data was generated from an Illumina machine)? Or is it more accurate to not even use any PON at all?
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