I am trying to compute breadth of coverage for exome data using cnvkit coverage command.
The output is in the form
chromosome start end gene depth log2 1 12098 12258 LOC102725121,DDX11L1 396.431 8.63093 1 12553 12721 LOC102725121,DDX11L1 402.667 8.65344 1 13331 13701 LOC102725121,DDX11L1 551.632 9.10756
reporting the coverage depth for each segment defined in first, second and third field.
At a first look it seems that the segments are non-overlapping (given the cnvkit pipeline I would say that it is definitely so), but I am unsure, because in the documentation I didn't find a detailed description the output of the
If so, it would speed the computation of coverage breadth. Are the segments non-overlapping?