It's not 100% clear to me that this is directly compatible with the graph reference, but if it isn't, that seems like a simple matter for Batzoglou & co. Those guys are really, really good, and the multi-reference target is a type of graph anyways, so I imagine it's just a bit more generalization (if any) to make BWBBLE work on a graph-structured reference assembly as implemented (there seem to be certain inconsistencies about how to represent structural variants that differ between implementations).

The other thing that would be neat is that then you'd have a direct tie-in to ancestral recombination graphs and could, in principle, get IBS/IBD for the same cost as high-confidence genotyping for any two individuals. Come to think of it, there's probably a way to recast this as shortest paths and get all admissible traversals between a population of genotyped individuals (given an ARG) for the same price as any two. Hmmm. This is a little disturbing.