RT Journal
A1 Chi, Eric C.
A1 Zhou, Hua
A1 Chen, Gary K.
A1 Del Vecchyo, Diego Ortega
A1 Lange, Kenneth
T1 Genotype imputation via matrix completion
JF Genome Research 
JO Genome Research 
YR 2013 
FD March 01 
VO 23 
IS 3 
SP 509 
OP 518 
DO 10.1101/gr.145821.112 
UL http://genome.cshlp.org/content/23/3/509.abstract 
AB 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 HapMap 3, simulated pedigree data, and simulated low-coverage sequencing data derived from the 1000 Genomes Project. Compared with leading imputation programs, the matrix completion algorithm 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.