Tutorial 1: How to perform Genome-Wide Association Studies (GWAS) with easyGWAS?

In this tutorial we demonstrate how to easily perform a genome-wide association study using the species Arabidopsis thaliana and two publicly available flowering time phenotypes.

To perform GWAS with easyGWAS you must first create an easyGWAS account. If you do not have an account, please create one and log in.

  1. First we navigate to the GWAS Center using the upper main navigation bar and click on New GWAS in the left navigation bar.

  2. Now we are in the GWAS wizard. This step-by-step procedure assists us to easily create new GWAS. In the first step we have to select a Species and a Dataset, as well as a Gene Annotation Set (optional). Here we see all publicly available Species and Datasets as well as all our privately uploaded Genotype data. In this tutorial we will select the Species Arabidopsis thaliana, the dataset AtPolyDB (call method 75, Horton et al.) and the Gene Annotation Set Gene Annotations (TAIR9). Then click Continue

  3. In the second step we have to select a Phenotype. Here we have the choice to select publicly available Phenotypes or private ones (if available) by searching the name of the phenotype using the autocompletion field. We can select a total of 5 Phenotypes. For this tutorial we select the two Phenotypes LD and LDV by typing their names. Then click Continue.

  4. In the following view we can see histograms of the phenotypic distributions and a p-value from the Shapiro-Wilk test. The Shapiro-Wilk-Test tests the null hypothesis that the data was drawn from a normal distribution. Here we can transform the phenotype by applying a transformation to the phenotype. The number of available transformations is automatically-determined and depends on the distribution of the selected Phenotypes. For our selected Phenotypes we choose a Log10 transformation and click Continue.

  5. To account for hidden confounding we can add Covariates or Principal Components to our experiments. However, this step is optional and in this tutorial we skip it by clicking Continue.
  6. Here we can either select all available SNPs for our analysis or we select a set of chromosomes. For our purpose, we select all SNPs and click Continue.

  7. Next we have to choose the algorithms and filters we would like to use for our analysis. First we select a Minor Allele Frequency Filter of 10%. Next we select, for each Phenotype, the algorithm EMMAX and click Continue.

  8. In the last step we are asked to confirm if all the parameters we chose for our analyses are correct. We can always adjust them, if necessary. Finally, we can submit our GWAS to the computation servers by clicking Submit GWAS.

Now all GWAS are submitted. We can monitor the current status of our GWAS at My temporary history. This view is updated automatically and we will get a notification via e-mail when the computations have finalized.