Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering.

By Sharon R. Browning, Brian L. Browning. American Journal of Human Genetics, 2007

3,116 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/dc965cec5e17db39602a8924eb1dcfc8af894d74

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Citations in the corpus

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data (2012, background): “, [30,31,32,33,34]) as in the 1000 Genomes project [7].”
Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP (2011, methodology): “For each of the ten maize chromosomes, the diploid marker data were phased and missing alleles imputed using the soft ware BEAGLE, version 3.3.1 (Browning and Browning, 2007).”
Genome-Wide Inference of Ancestral Recombination Graphs (2013, methodology): “Our methods may also be useful for a wide variety of related applications, including local ancestry inference [47,93,94], haplotype phasing/genotype imputation [46,48,95,96], and recombination rate estimation [22,97].”
GWAMA: software for genome-wide association meta-analysis (2010, methodology): “Meta-analysis of GWA studies has been greatly assisted by the development of imputation techniques [5,6] which predict genotypes not directly typed on available GWA genotyping products, but which are present on a dense reference panel of haplotypes, such as those available as part of the…”
A genetic variant near olfactory receptor genes influences cilantro preference (2012, methodology): “For all participants, we imputed genotypes in batches of 8,000–10,000 using Beagle and Minimac [31, 32, 33] against the August 2010 release of the 1000 Genomes reference haplotypes [34], as described in [35].”
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 Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies (2009, methodology): “The BEAGLE imputation model [12,13] is one notable exception to this point, and we discuss its alternative modeling strategy in detail in this work.”
vcfr: a package to manipulate and visualize variant call format data in R (2017, methodology): “Phasing was performed with BEAGLE 4 (Browning & Browning 2007).”
LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms (2015, methodology): “…there have been comparisons between generic imputation methods (Stekhoven and Bühlmann 2012; Rutkoski et al. 2013) and between genotype-speci ﬁ c methods (Browning and Browning 2007; e.g. , Marchini and Howie 2010), there has been little comparison be-tween the two groups of algorithms to date.”
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells (2016, neutral): “…Li, 2011 https://github.com/SAMtools/SAMtools/releases/tag/1.2 VQSR DePristo et al., 2011 https://www.broadinstitute.org/gatk/guide/article?id=39 BEAGLE r1398 Browning and Browning, 2007 https://faculty.washington.edu/browning/beagle/ PLINK v1.”