A basic 'first-pass' at a GWAS. To run the pipeline, follow the workflow in GWASPipeline.Rmd. There are more thorough descriptions of each step in the Sandpit directory, with relevant references in the References directory. A full working example will be added to the ExampleDatasets directory shortly.
The GWASPipeline does the following:
- QC Genotypes (from either VCF or BCF files)
- Determine the population structure (naive approach currently, to be refined in future)
- perform a standard GWAS using plink
- saves the results of the association tests, produces Q-Q plots and a manhattan plot.
We assume that the trait files have already been created and QC'd.