GEDI- Genotype Error Detection and Imputation


The GEDI package provides methods for

  • error detection in whole-genome SNP genotype data
  • recovery of missing SNP genotypes
  • imputation of genotypes at untyped SNPs based on reference haplotypes such as those provided by the Hapmap project

Additionally, the GEDI package includes a copy of our highly scalable ENT algorithm for genotype phasing. GEDI handles genotype data from unrelated individuals as well as individuals related by simple pedigrees such as trios. GEDI computations rely on efficient likelihood computations based on a Hidden Markov Model of haplotype diversity in the population under study.

GEDI source code

Contact Information

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Acknowledgment and Disclaimer

This material is based upon work supported in part by the National Science Foundation under Grants No. IIS-0546457, IIIS-0916948 and DBI-0543365. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.