As referenced in the pvcf documentation… what are overlapping variants? https://www.biorxiv.org/content/biorxiv/early/2018/06/11/343970.full.pdf
Hybrid allelic representation. To facilitate downstream summary statistics without doublecounting, ideal unified sites would be completely nonoverlapping, with mutually-exclusive alleles.
I understand snv, insertion, deletion, copy number… but what does an overlap look like? I can’t find any descriptive information aside from mentions that “variants can overlap.”
Is this when a single mutation is represented multiple ways by different ordering of alleles?