Dear all,
I'm trying to perform CNV with matched tumor-normal pair. 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, possibly 15, 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 neutral LOH in my samples?
Or I can be confident only about Chr. X, 19 and 17 where CR plot and AF plot seems to demonstrate the same things?
Thanks in advance!
Best, Eugene
To evaluate your output you can use a gene-based comparison. For the gene-based comparison, you should first annotate the detected CNV segments in the benchmark and samples. We can use “cghMCR” R package from Bioconductor to identify CNV genes using Refseq gene identifications. The average of the CNV values of the overlapping CNV segments for each gene can be used as the gene CNV value. A threshold of ± thr for log2 ratios was used for calling CNV genes, that is: amplification for log 2 ratios > thr, deletion for log 2 ratios
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