Genotype imputation via matrix completion
- 1 University of California, Los Angeles;
- 2 North Carolina State University;
- 3 University of Southern California
- ↵* Corresponding author; email: eric.c.chi{at}gmail.com
Abstract
Most current genotype imputation methods are model-based and computationally intensive, taking days to impute one chromosome pair on 1000 people. We describe an efficient genotype imputation method based on matrix completion. Our matrix completion method is implemented in Matlab and tested on real data from HapMap3, simulated pedigree data, and simulated low-coverage sequencing data derived from the 1000 Genomes Project. Compared to leading imputation programs, matrix completion as embodied in our program Mendel-Impute achieves comparable imputation accuracy while reducing run times significantly. Implementation in a lower-level language such as Fortran or C is apt to further improve computational efficiency.
- Received July 11, 2012.
- Accepted December 3, 2012.
- © 2012, Published by Cold Spring Harbor Laboratory Press
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
