Association Studies

• Genome-Wide Association Studies (GWAS) with PLINK
• Use Cases
• Summary
• Inputs
• Outputs
• Workflow Walkthrough
• Citations
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Genome-Wide Association Studies (GWAS) with PLINK

Version: v0.0.1

Use Cases

Determine association between a trait and genotypes. Association is a statistically significant difference in genotype between affected individuals (those with the trait) and unaffected individuals (those without the trait).

Summary

This workflow uses PLINK [12] to determine associations between traits and genotypes. This workflow removes position and samples with too much missing data (> 95%), positions with minor allele frequency (threshold 0.05) and uses HWE to filter out all variants which have Hardy-Weinberg equilibrium exact test p-value below the provided threshold (default 0.001). Population stratification is determined by complete linkage clustering using IBS calculations. Positions exhibiting excessive linkage disequilibrium are removed. Finally association is calculated using fisher exact tests.

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