A linear complexity phasing method for thousands of genomes

By Olivier Delaneau, Jonathan Marchini, Jean-François Zagury. Nature Methods, 2011

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View Paper: https://www.semanticscholar.org/paper/df4fa68067840626e6196d14e610c8b6f820a516

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Citations in the corpus

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness (2014, methodology): “We recently compared several methods all designed to phase nominally unrelated samples (SHAPEIT2 [2], SHAPEIT1 [5], Beagle [4], HAPI-UR [6], Impute2 [24], MaCH [25], fastPHASE [26]) and found that SHAPEIT2 was the most accurate method in this setting.”
High density genetic mapping identifies new susceptibility loci for rheumatoid arthritis (2012, background): “Among 38 rheumatoid arthritis–associated SNPs or proxies accessed for expression quantitative trait loci (eQTL) analysis, 18 showed an eQTL effect on at least one probe, giving a total of 51 SNP-probe combinations with a significant eQTL effect ( Supplementary Table 13 ).”
Reference-based phasing using the Haplotype Reference Consortium panel (2016, methodology): “Over the past decade, phasing has most commonly been performed via statistical methods applied within a genotyped cohort [2–14].”
Fast and accurate long-range phasing in a UK Biobank cohort (2015, neutral): “Most existing methods for statistical phasing apply hidden Markov models (HMM) to iteratively refine haplotype frequency models and improve phase calls [6–12].”
A method for genome-wide genealogy estimation for thousands of samples (2019, methodology): “Mutations with activity period in [10,50) KYBP.”
WhatsHap: fast and accurate read-based phasing (2016, methodology): “SHAPEIT [6] is an example of a software for statistical, population-based phasing and Merlin [7] for genetic, pedigree-based phasing.”
Next-generation genotype imputation service and methods (2016, methodology): “Similar ideas are a fundamental part of haplotype sharing analyses and have been used in Beagle 16 , SHAPEIT 17,18 , and other genomics tools 19–21 to improve computational performance.”