GIGI-Pick

GIGI-Pick

Subject Selection for Sequencing in Pedigrees

Introduction

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.

Reference

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.

Download

The latest version of GIGI-Pick, along with example files, is available here (current version: 0.91).      [documentation].
Please use GIGI-Pick version 0.91 or later. The program is written in C++ and runs on Linux machines.

Dependencies

This program currently depends on gl_auto output from MORGAN version 3.1.1. You can download MORGAN version 3.1.1 here. The gl_auto version 3.1.1 tutorial is available here.

Support for MORGAN version 3.2 will soon be available. For more information, please refer to Professor Elizabeth Thompson's MORGAN

Contact

Method developer & maintainer: Charles Y K Cheung - cykc@uw.edu

This work was supervised by Professor Ellen M. Wijsman


last updated: February 7, 2014