Prabhakaran (2011) HIV haplotype inference using a constraint-based DPM
This paper extends SHORAH to better infer global haplotypes.
The work is a collaboration between Niko Beerenwinkel’s group and Volker Roth’s group. Roth is at the the U Basel computer science department. Other authors are Melanie Rey, Osvaldo Zagordi, Huldrych Günthard, and Karin Metzner.
the paper really isn’t clear on how they move from local to global reconstruction.
They introduce the following soft constraint. If two reads are assigned to different local haplotypes (i.e. differ in their local window) then they must be assinged to different haplotypes at the global level. Such do-not-link constraints are incorporated into the prior distribution of the subequent class assignments