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Bioinformatics. 2012 Sep 15;28(18):2397-9. Epub 2012 Jul 13.

GAPIT: genome association and prediction integrated tool.

Author information

  • 1Computational Biologist with the United States Department of Agriculture - Agricultural Research Service, Ithaca, NY 14853, USA.

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.

PMID:
22796960
[PubMed - indexed for MEDLINE]
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