In VG, a variant is defined as (contig/pos/ref/alt/svlen) so del/dup differing by 1% is regarded as a different variant.
I kind of thing perhaps they should do this in a VCF, but we can't really enforce that.
Analysis
So, perhaps, we need to solve this, I think things with zygosity filters (cohort/trio/quad/compound het) etc could have a special cases for it
Variant Details
The SVs would appear in same for this locus at the bottom if they only vary in END position, varying per start they would not be there.
Perhaps we need a "nearby" SV overlap section
In VG, a variant is defined as (contig/pos/ref/alt/svlen) so del/dup differing by 1% is regarded as a different variant.
I kind of thing perhaps they should do this in a VCF, but we can't really enforce that.
Analysis
So, perhaps, we need to solve this, I think things with zygosity filters (cohort/trio/quad/compound het) etc could have a special cases for it
Variant Details
The SVs would appear in same for this locus at the bottom if they only vary in END position, varying per start they would not be there.
Perhaps we need a "nearby" SV overlap section