Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering.
This work presents a new method and software for inference of haplotypes phase and missing data that can accurately phase data from whole-genome association studies, and presents the first comparison of haplotype-inference methods for real and simulated data sets with thousands of genotyped individuals.
A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals.
Genotype Imputation with Millions of Reference Samples.
A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic
It is demonstrated that resequencing studies can identify important genetic associations, provided that specialised analysis methods, such as the weighted-sum method, are used.
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data
Refined IBD allows for IBD reporting on a haplotype level, which facilitates determination of multi-individual IBD and allows for haplotype-based downstream analyses and is implemented in Beagle version 4.
A One-Penny Imputed Genome from Next-Generation Reference Panels.
A fast, powerful method for detecting identity by descent.
A one penny imputed genome from next generation reference panels
A new genotype imputation method, Beagle 5.0, is presented, which greatly reduces the computational cost of imputation from large reference panels and is compared with Beagle 4.1, Impute4, Minimac3, andMinimac4 using 1000 Genomes Project data, Haplotype Reference Consortium data, and simulated data.
Haplotype phasing: existing methods and new developments
The haplotype phasing methods that are available are assessed, focusing in particular on statistical methods, and the practical aspects of their application are discussed, and recent developments that may transform this field are described.