Assessment of genotype imputation methods

  title={Assessment of genotype imputation methods},
  author={Joanna M. Biernacka and Rui Tang and Jia Li and Shannon K. McDonnell and Kari G. Rabe and Jason P. Sinnwell and David N. Rider and Mariza de Andrade and Ellen L. Goode and Brooke L. Fridley},
  booktitle={BMC proceedings},
Several methods have been proposed to impute genotypes at untyped markers using observed genotypes and genetic data from a reference panel. We used the Genetic Analysis Workshop 16 rheumatoid arthritis case-control dataset to compare the performance of four of these imputation methods: IMPUTE, MACH, PLINK, and fastPHASE. We compared the methods' imputation error rates and performance of association tests using the imputed data, in the context of imputing completely untyped markers as well as… CONTINUE READING


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