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somatic CNV PoN
When I run the CNV somatic paired workflow, should I exclude the paired normal sample in PoN?
Previously @shlee said I need to do the germline CNV extraction manually after I get the segment results from both tumor and normal. https://gatkforums.broadinstitute.org/gatk/discussion/24229/call-paired-somatic-cnv#latest
The problem here is when I include my normal sample in the PoN, the final CNV calls for the normal sample seem to have nothing. So I don't have anything to remove from the tumor. I think the program treated most of the points in my normal sample as noise so it removed them, but not all points. I can still see some sparse points on the normal sample plot. It seems to help me remove most of the germline CNVs.
1. Do you recommend to remove the paired normal sample when creating PoN.
2. If I include the paired sample in my PoN, do you think it is good enough to remove germline CNVs?
Segment plot when I include this normal sample in PoN:
The paired tumor sample: