Can someone recommend software for reference-based genotype-estimation?
In case anyone was interested, a new piece of software for rapidly imputing and phasing low coverage sequence data from genotype likelihoods has just been released. It is called GLIMSPE and is exactly what I was after. 

It looks to be much faster (1200x speedup) compared to Beagle 4.0, and is more accurate at imputing low frequency variants. It is also more amenable to use with larger reference panels (such as the Haplotype Reference Consortium panel).