I was performing CNV calling with cnvKIT and pureCN on targeted RNA-Seq data. Both use the CBS-algorithm for segmentation. The segments are usually uniform over all chromosomes, except for one specific gap. I am trying to figure out, what caused this. The coverage of the targets surrounding the gap is not lower compared to other regions on this chromosome.
Any Idea why there is a gap in this place?
Any Idea why there is a gap in this place?