To achieve this haplotype phasing and genotype calling, HMM-based phasing methods that were primarily designed to estimate haplotypes from SNP array data were adapted to deal with sequencing data. For example, the 1000GP Phase 1 set of haplotypes from 1,092 individuals was estimated using a combination of Beagle [3] and MaCH/Thunder [4]. Such haplotype reference panels are now routinely used to impute unobserved genotypes in GWAS studies, as this increases power to detect and resolve associated variants and facilitates meta-analysis [5].
