Improving the Accuracy and Efficiency of Identity by Descent Detection in Population Data
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Cites methods from "Improving the Accuracy and Efficien..."
...The name was originally shorthand for “population linkage”; BEAGLE: A software package capable of high-accuracy haplotype phasing, genotype imputation, and identity-by-descent estimation, developed by Browning [2]; GCTA: Genome-wide Complex Trait Analysis....
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...To support easier interoperation with newer software, for example BEAGLE 4 [2], IMPUTE2 [3], GATK [4], VCFtools [5], BCFtools [6] and GCTA [7], features such as the import/export of VCF andOxford-format files and an efficient cross-platform genomic relationship matrix (GRM) calculator have been introduced....
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...Browning, B., Browning, S.: A fast, powerful method for detecting identity by descent....
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...Browning, B.: Presto: rapid calculation of order statistic distributions and multiple-testing adjusted p-values via permutation for one and two-stage genetic association studies....
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...Browning, B., Browning, S.: Improving the accuracy and efficiency of identity by descent detection in population data....
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"Improving the Accuracy and Efficien..." refers methods in this paper
...Probabilistic methods including Beagle IBD (Browning and Browning 2010), IBD_Haplo (Brown et al. 2012), RELATE (Albrechtsen et al. 2009), IBDLD (Han and Abney 2011), and PLINK (Purcell et al. 2007) fit a hidden Markov model (HMM) for IBD status and determine posterior probabilities of IBD....
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"Improving the Accuracy and Efficien..." refers background or methods in this paper
...…history (Campbell et al. 2012; Gusev et al. 2012; Palamara et al. 2012; Ralph and Coop 2012), IBD mapping (Purcell et al. 2007; Gusev et al. 2011; Browning and Thompson 2012), and heritability analysis in founder populations (Price et al. 2011; Zuk et al. 2012; Browning and Browning 2013)....
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...We analyzed 500 individuals of the simulated unphased filtered sequence data, using Refined IBD with a minimum segment length of 0.2 cM and LOD scores of 4 and 5....
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