Biostatistics 666: Advanced Haplotype Estimation
This lecture introduces modern methods for haplotype estimation, which based on an idea introduced by Na Li and Matthew Stephens in 2003. This approach models each haplotype in the sample as an imperfect mosaic of other haplotypes. It typically favors solutions that involve longer mosaic pieces and where there are fewer mismatches between each haplotype and its template.
Li and Stephens (2003) Genetics 65:2213-33.
Li et al (2010) Genetic Epidemiology 34:816–34