GIGI: Genotype Imputation Given Inheritance


Subject Selection for Sequencing in Pedigrees


GIGI-Pick is a computer program that facilitates the evaluation and comparison of subject selection choices in sequencing studies in pedigrees. This program uses a "coverage" as one metric to naturally relate pedigree-based genotype imputation to subject selection. This metric enables the use of inferred inheritance vectors (IVs) to optimize imputation of alleles in candidate regions when such information is available. Our approach can incorporate information about IVs to guide subject selection for sequencing. If a candidate region is not available, a variant of this metric may be used to optimize selection genome-wide.


Cheung CYK, Blue EM, Wijsman EM (2014) A statistical framework to guide sequencing choices in pedigrees. American Journal of Human Genetics 94:257-267.[link]

Disclaimer and future directions

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


The latest version of GIGI-Pick, along with example files, is available here (current version: 1.06).      [documentation].
Please use GIGI-Pick version 1.06 or later. The program is written in C++ and runs on Linux machines.


With this release, GIGI-Pick 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.


Method developer: Charles Y K Cheung> - or supervisor: Ellen M Wijsman .

This work was supervised by Professor Ellen M. Wijsman

last updated: February 17, 2019