copy number of gene in the gap of segmentation file
I have a basic question for CNV segment output from Sequenza for WES data from paired tumor/normal samples.
There are always some gap between nearly segments, such as below example gap (17: 41165610-41368081) between these two samples on chr17.
17 30671151 41165609
17 41368082 41465708
How do we understand the copy number status in this segment gap, say chr17: 41165610-41368081? I checked the bam file and it seems we cannot simply consider this is CN=0 region for tumor. And it is really important because some key gene such as BRCA1 is in this gap region.
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