Hi, I am trying to call somatic CNVs on targeted panel of ~ 525 genes using GATK somatic CNV pipeline. I do not have a matched normal for the tumor sample. To help with denoising, I am looking to create a panel of normals (PoN) for somatic CNV calling.
I had a few questions related to PoN creation :
- The minimum recommended number of samples is 40 for WES according to documentation by GATK team. Would 40 samples be sufficient number of samples for creation of PoNs for calling somatic CNV on targeted panel of 525 genes?
- The type of sample recommended in the documentation is blood normals with no large CNV events. Our assay has a mixture of cytology and FFPE. Would mixing multiple sample types (cytology, FFPE) be okay for creation of PoNs?
- Is it alright to use normals that are tumor tissue but silent for CNVs for creation of PoNs?
The documentation recommends using different set of PoN for different sequencing platforms. Would there be recommendation for creation of PoNs when there is variability in
- Coverage variability due to underfilling of flowcells resulting in high coverage in few samples
- Flow cell type I.e., (S1,S2, Sprime) i.e., normals coming from different flowcell types
- Is there a resource bundle for hg19 build for WES CNV PON hdf5 ?
- Does GATK somatic CNV pipeline exclude normals in PoNs based on match to test samples profile?
- Is there range of purity of sample(test) at which GATK somatic CNV pipeline performs best?
Please let me know. Thanks in advance for your help and looking forward to hearing from the GATK team.
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