GEDI-ADMX Genotype error detection and imputation for admixed populations
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GEDI-ADMX Description

GEDI-ADMX is an application built to handle genotype data from unrelated individuals. Local ancestry inference uses a factorial HMMs trained on ancestral haplotypes to impute genotypes at all typed SNP loci under each possible local ancestry. GEDI-ADMX assigns to each locus the local ancestry that yields the highest imputation accuracy, as assessed using a weighted-voting scheme based on multiple SNP windows centered on the locus of interest. Error detection and imputation of missing genotypes at typed SNPs is performed using multilocus genotype probabilities computed based on the factorial HMM corresponding to the inferred local ancestry. Imputation of genotypes at each untyped SNP is performed based on posterior genotype probabilities computed using a similar factorial HMM spanning k (default k=10) typed SNPs before and after the imputed locus. The GEDI-ADMX package provides methods for: · local ancestry inference · SNP genotype error detection and correction · imputation of missing genotypes at typed SNPs, and · imputation of genotypes at untyped SNPs.

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