GIGI: Genotype Imputation Given Inheritance

GIGI: Genotype Imputation Given Inheritance


GIGI is a computer program to impute missing genotypes on pedigrees. Our approach handles large pedigrees by using a Markov Chain Monte Carlo-based program to infer inheritance vectors. Our approach has 2 steps:

  1. use the program gl_auto from the MORGAN package to infer inference vectors
    • using genotypes from informative framework markers
  2. use GIGI to impute missing genotypes



The latest version of GIGI, along with example files, is available here (current version: 1.04).      [documentation][FAQs][changelog].
The program is written in C++ and runs on Linux machines.

Older version: v1.03 [documentation]

Older version: v1.02


GIGI is for imputing genotypes on pedigrees with known pedigree structure. If the goal is to impute genotypes on unrelated individuals, consider using a population-based genotype imputation program (eg. BEAGLE) instead.


Programmer and maintainer: Charles Y K Cheung -

last updated: Nov. 15, 2013