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. 2012 Sep 15;28(18):2397-9.
doi: 10.1093/bioinformatics/bts444. Epub 2012 Jul 13.

GAPIT: genome association and prediction integrated tool

Alexander E Lipka  1 , Feng Tian, Qishan Wang, Jason Peiffer, Meng Li, Peter J Bradbury, Michael A Gore, Edward S Buckler, Zhiwu Zhang
Affiliations

GAPIT: genome association and prediction integrated tool

Alexander E Lipka et al. Bioinformatics. .

Abstract

Summary: Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power, provide high prediction accuracy and run in a computationally efficient manner. We developed an R package called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10 000 individuals and 1 million single-nucleotide polymorphisms with minimal computational time, while providing user-friendly access and concise tables and graphs to interpret results.

Availability: http://www.maizegenetics.net/GAPIT.

Contact: zhiwu.zhang@cornell.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

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