Detection of Mendelian Consistent Genotyping Errors
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.
ReferenceCheung, CYK., Thompson, E.A., Wijsman, E.M. (2014) Detection of Mendelian Consistent Genotyping Errors in Pedigrees. Genetic Epidemiology 38(4):291-299. [link]
DisclaimerGIGI-Pick is in beta version. If you find any bugs, please contact us.
With this release, GIGI-Check is now compatible with MORGAN version 3.2. You can download MORGAN version 3.2 and find links to a user tutorial here
We no longer support MORGAN version 3.1.1, but the gl_auto version 3.1.1 tutorial is available here for users who have files in this older format.
last updated: February 2, 2015