alt aware analysis tools?

Question

[Richard]

Hi all,

I've seen that BWA now provides some analysis tools to help take advantage of alt contigs in the the human reference.

If one was interested in including the alt contigs in analysis, are there any other aligners/variant callers that could be collected into an alt-aware pipeline?

From what I can tell, BWA seems to be the only tool to deal the presence of alt contigs specifically, though I'm hoping there are others out there that I'm missing.