I am wondering how to call for variants if I don't have the normal matched sample. I have read that the key here is the Panel of Normals (PONs), as mentioned in: https://gatk.broadinstitute.org/hc/en-us/community/posts/360057810051-Mutect2-somatic-variant-calling-with-without-matched-normal-sample
I have two scenarios due to my cohorts in my project.
#1. Patients with Normal and Tumor Tissue and cfDNA, everything matching, so from every patient I have these three. I am interested in the somatic mutations in both tumor tissue and cfDNA. For the first one, no problem, I run Mutect2 in Tumor with matched-Normal mode and somatic variants were successfully detected in tissue.
What about the cfDNA? Can I use the Normal tissue samples from each patient to create its corresponding PONs? Is there any other approximation or this is the correct one?
#2. Patients that only have cfDNA, no tissue biopsies. What can I do here? I don't have any normal sample from these patients, so how can I create the PONs? These patients differe from patients in #1, so, would it be correct to make a "mix" from normal samples in #1 in order to create a PONs? Is it better to use external data from normal samples?
I know that there is no a standard pipeline to analyze cfDNA, but what I want to know is about the PONs here
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