Note on callCNVs.py – backtrack_aggregateCalls Function

[septiera]

In the function backtrack_aggregateCalls, we are currently redefining the boundaries for consecutive CNVs that have different copy number variations but are merged due to their hidden state. This occurs especially with homodeletions and heterodeletions. Here, the boundaries for heterodeletions are extended to those of homodeletions, which results in two distinct calls. This suggests a scenario where a short heterodeletion on one allele might extend longer on the second allele, creating a common region that appears as a homodeletion.

Should we reconsider how we define and merge these boundaries to better capture the nuances of CNV events? This might help in accurately delineating distinct genomic alterations.