For generating custom panel-specific resources, what is the ideal scenario of tumor and normal samples to be included? The documentation suggests minimum 20 samples (tumor?). What happens if I have 10? Can these samples be part of the test data or do they have to be independent? And I’m also unclear about “Panel artefact PON”. Are these supposed to be tumor-specific artefacts from the above samples or germline events from the normal samples for filtering variants? Do I also need additional normal samples to create panel-specific germline events? If I also want to target RNA events in my panel, do I also need paired RNA-seq data for those >=20 samples for TPM normalisation? What if I use non-paired RNA samples? The doc says “files from a representative set of sample” but what if I have FFPE samples where RNA quality is bad and cannot be sequenced?

Generally, a Panel of Normals means a set of (germline) samples unrelated to your clinical cancer samples or research cohort. If you need to re-use normal samples from cancer patients make sure none of the normals have cancer-related predispositions.

Yes agreed, and I have unrelated confirmed normal samples, then how can I feed them into the oncoanalyser pipeline?