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Interpreting of CNV pipeline results
Dear GATK team, first af all thanks a lot for the very detailed manual for CNV calling it was super helpfull!
Second - I'd like to ask an advise on results interpretation.
I'm trying to perform CNV with matched tumor-normal pair, but without a PON (I do not have enough of my own samples to construct one, and not sure that samples that I could download will performe better then matched normal). To complicate things it seems that my tumor sample is strongly contaminated with normal tissue (that I've already learned from Mutect2 results)
After running the pipeline (https://gatkforums.broadinstitute.org/dsde/discussion/11682,
https://gatkforums.broadinstitute.org/dsde/discussion/11683) with default paramiters (for starters) I'm getting the following output (please see the attached image).
I'm not quite sure how to interpret situation when according to the AF plot, it seems that my sample has a copy loss for the entire chrom. 7 and 14, and partiall loss of chrom. 4 but on the other hand there are no evidence for that on CR plot. Similary it seems that there is a copy number changes for chr. 20 in CR plot but there are no evidence for that on AF plot.
Does it mean that there are copy nutral LOH in my samples?