PLINK (genetic tool-set)
PLINK[1] is a free, commonly used, open-source whole genome association analysis toolset designed by Shaun Purcell. The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses.
PLINK currently supports following functionalities:
- data management;
- basic statistics;
- Linkage disequilibrium (LD) calculation;
- Identity by descent (IBD) and identity by state (IBS) matrix calculation;
- population stratification;
- association analysis such as Genome-wide association study for both basic case/control studies and quantitative traits.
Extensions and current developments
- PLINK 2.0 a comprehensive update to PLINK, developed by Christopher Chang, with the improved speed of various Genome-wide association (GWA) calculations, including identity-by-state (IBS) matrix calculation, LD-based pruning and association analysis.
- PLINK/SEQ is an open-source C/C++ library designed for analyzing large scale whole-genome and whole-exome studies.
- MQFAM is a multivariate test of association (MQFAM) that can be efficiently applied to large population-based samples and is implemented in PLINK.
References
- ↑ Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007). "PLINK: a toolset for whole-genome association and population-based linkage analysis.". American Journal of Human Genetics. 81: 559–75. doi:10.1086/519795. PMC 1950838
. PMID 17701901.
External links
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