PLINK Association workflow

PLINK is an open-source genome association analysis (GWAS) suite of tools providing a range of basic, large-scale computationally-efficient analyses. PLINK may be used for analysis of genotype/phenotype data, but requires some outside data-preprocessing (e.g., study design and planning, generating genotype or CNV calls from raw data). Support for visualization, annotation and storage of results is provided via gPLINK and Haploview.

The PLINK Association workflow provides testing for disease traits using comparing allele frequencies between cases and controls (asymptotic and empirical p-values are available). Specifically it provides the Cochran-Armitage trend test, Fisher's exact test, different genetic models (dominant, recessive and general), tests for stratified samples (e.g. Cochran-Mantel-Haenszel, Breslow-Day tests), a test for a quantitative trait; a test for differences in missing genotype rate between cases and controls; multilocus tests, using either Hotelling's T(2) statistic or a sum-statistic approach (evaluated by permutation) as well as haplotype tests. The basic tests can be performed with permutation, described in the following section to provide empirical p-values, and allow for different designs (e.g. by use of structured, within-cluster permutation).

URL: http://www.loni.ucla.edu/twiki/bin/view/CCB/PipelineWorkflows_BioinfoPLINK

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