GLASCOW performs genome-wide association studies using Generalized Linear Mixed Models (GLMM) and a score test as described in Zhang et al. Association is performed between factors (SNPs or haplotypes) and a phenotype (with different type of distributions:normal, binomial, counts). The method relies on two steps. In the first one, a GLMM without the factor of interest is solved (including estimation of variance components and of fixed and random effects solutions) and residuals are computed. In the second step, the residuals are used to test significance of association between the factor and the phenotype at each position along the genome (or the selected data).
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Bioinformatics. 2012 Oct 1;28(19):2467-73. Epub 2012 Jun 17.
Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification.
Zhang Z, Guillaume F, Sartelet A, Charlier C, Georges M, Farnir F, Druet T.