GIGI: Genotype Imputation Given Inheritance

Introduction

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

Reference

• Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2013). GIGI: An approach to effective imputation of dense genotypes on large pedigrees. American Journal of Human Genetics 92:504-516 [link]

Download

GIGI, along with example files, is available here [documentation][FAQs]. (current version: 1.02)
The program is written in C++ and runs on Linux machines.

Note

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.
 

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last updated: March 6, 2013