A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants

@inproceedings{Yang2014ANG,
  title={A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants},
  author={Yumei Yang and Qishan Wang and Qiang Chen and Rongrong Liao and Xiangzhe Zhang and Hongjie Yang and Youmin Zheng and Zhiwu Zhang and Yuchun Pan},
  booktitle={PloS one},
  year={2014}
}
We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy… CONTINUE READING
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