GIGI-Check

Detection of Mendelian Consistent Genotyping Errors

Introduction

GIGI-Check is a C++ program to detect Mendelian consistent genotyping errors of dense markers in pedigree data. It detects genotyping errors by using Inheritance Vectors (IVs), which are inferred by using sparse framework genotypes available on a subset of relatives in the pedigree. Thus, our error detection approach consists of two steps. The first step is to infer IVs at the positions of framework markers using gl_auto, a MCMC-based program from the MORGAN package. We assume that these markers are free of genotyping errors. The second step is to detect errors in dense genotypes by GIGI-Check using the IVs and pedigree structure file from MORGAN.

Reference

Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2014) Detection of Mendelian Consistent Genotyping Errors in Pedigrees. Genetic Epidemiology 38(4):291-299. [link]

Download

GIGI-Check, along with example files, is available here (current version: 1.06) [documentation].
The program is written in C++ and runs on Linux machines.

Disclaimer

GIGI-Pick is in beta version. If you find any bugs, please contact us.

Dependencies

With this release, GIGI-Check is now compatible with MORGAN version 3.2 or more recent. You can download MORGAN and find links to a user tutorial here

We no longer support MORGAN version 3.1.1.

Contact

Method developer: Charles Y K Cheung - cykc@uw.edu or supervisor: Ellen M. Wijsman .

This work was supervised by Professor Elizabeth A. Thompson and Professor Ellen M. Wijsman

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last updated: February 17, 2019