O'Connell, J. et al. PLoS Genet. 10, e1004234 (2014).

Going from single-nucleotide polymorphism (SNP) genotype to a haplotype (the SNPs specific to one chromosome) requires statistical methods. Previous approaches to phasing, the determination of a haplotype, for individuals in a cohort have required knowledge about the relatedness of the individuals. Most methods assume no relatedness; some can deal with a predefined level of connections such as family trios. O'Connell et al. now present an approach that allows phasing at any level of relatedness. First they used SHAPEIT2 to infer a haplotype while ignoring all information about familial connections. Then they used a hidden Markov model (duoHMM) to infer the inheritance pattern from the SHAPEIT2 data and any available family information. Not only is this combined method highly accurate, it can also detect genotyping errors and infer recombination events in duos and trios.