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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. Expand
A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals.
It is demonstrated that substantial gains in imputation accuracy accrue with increasingly large reference panel sizes, particularly when imputing low-frequency variants, and that unphased reference panels can provide highly accurate genotype imputation. Expand
Genotype Imputation with Millions of Reference Samples.
A genotype imputation method that scales to millions of reference samples and achieves fast, accurate, and memory-efficient genotypes imputation by restricting the probability model to markers that are genotypes in the target samples and by performing linear interpolation to impute ungenotyped variants. Expand
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. Expand
A fast, powerful method for detecting identity by descent.
It is shown that it is possible to use fastIBD to generate highly accurate estimates of genome-wide IBD sharing between pairs of distant relatives, which is useful for estimation of relationship and for adjusting for relatedness in association studies. Expand
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. Expand
A One-Penny Imputed Genome from Next-Generation Reference Panels.
- B. Browning, Ying Zhou, S. Browning
- Mathematics, Medicine
- American journal of human genetics
- 6 September 2018
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 and Impute4 using 1000 Genomes Project data, Haplotype Reference Consortium data, and simulated data. Expand
Efficient multilocus association testing for whole genome association studies using localized haplotype clustering
A combined single‐marker and haplotypic strategy is proposed, in which both single‐ Marker and Haplotypic tests are applied, with the minimum P‐value adjusted for multiple testing by permutation which results in a test that is powerful for detecting both low‐and high‐frequency disease‐susceptibility variants. Expand
Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.
Results from single-marker and haplotypic analysis of the BEAGLE method's genotype calls for the bipolar disorder study indicate that the method is highly effective at eliminating genotyping artifacts that cause false-positive associations in genome-wide association studies. Expand
High-resolution detection of identity by descent in unrelated individuals.
A method for detection of recent IBD in population samples is presented and it is found that the method can detect segments of a length of 2 cM with moderate power and negligible false discovery rate in Illumina 550K data in Northwestern Europeans. Expand