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?
here are two variants from gnomad:

    1	13459	rs1315857414	CAGA	C
    1	13462	rs1441058751	AAGT	A

as you can see, the first variant CAGA at 13459 overlaps with th position 13462
