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GAPIT: genome association and prediction integrated tool
Open accessAbstract
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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Variance component model to account for sample structure in genome-wide association studies
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Huang, M., Liu, X., Zhou, Y., Summers, R. M., & Zhang, Z. (2019) · GigaScience · doi:10.1093/gigascience/giy154 · Cited by 855
Self-citationThe barley pan-genome reveals the hidden legacy of mutation breeding
Jayakodi, M., Padmarasu, S., Haberer, G., Bonthala, V. S., Gundlach, H., Monat, C., Lux, T., Kamal, N., Lang, D., Himmelbach, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2947-8 · Cited by 565
Status and prospects of genome‐wide association studies in plants
Tibbs Cortes, L., Zhang, Z., & Yu, J. (2021) · The Plant Genome · doi:10.1002/tpg2.20077 · Cited by 470
Self-citationAlqudah, A. M., Sallam, A., Stephen Baenziger, P., & Börner, A. (2020) · Journal of Advanced Research · doi:10.1016/j.jare.2019.10.013 · Cited by 432
Genebank genomics highlights the diversity of a global barley collection
Milner, S. G., Jost, M., Taketa, S., Mazón, E. R., Himmelbach, A., Oppermann, M., Weise, S., Knüpffer, H., Basterrechea, M., König, P., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0266-x · Cited by 420
Metadata
- Authors
- Lipka, A. E., Tian, F., Wang, Q., Peiffer, J., Li, M., Bradbury, P. J., Gore, M. A., Buckler, E. S., & Zhang, Z.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-07-13
- Volume
- 28
- Issue
- 18
- Pages
- 2397-2399
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2161620511
- Cited by
- 2,257
- References
- 4
- FWCI
- 23.56
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Lipka, A. E., Tian, F., Wang, Q., Peiffer, J., Li, M., Bradbury, P. J., Gore, M. A., Buckler, E. S., & Zhang, Z. (2012). GAPIT: genome association and prediction integrated tool. Bioinformatics. https://doi.org/10.1093/bioinformatics/bts444
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