Genome-wide Association Studies using the Discovery Environment

Rationale and background:

GWAS refers to analysis of the genomic architecture underlying a trait of interest. 

Using TASSEL

Step 1: Run MLM Workflow

Locate the TASSEL 4.0.3 (MLM) Application under

Public Apps->QTL and GWAS->Models and Workflows

In the Select Input Data section click on the Browse button next to the Select Marker File. Locate the input files under

'Community Data'->iplant_training->advanced_gwas->input

and select the file named "mdp_genotype.hpm.txt".
In the list box labeled "Select marker file format" leave the value "Hapmap".

Repeat the same process for the trait file (mdp_traits.txt), the kinship (mdp_kinship.txt) and the population structure file (mdp_population_structure.txt).

In the Options section, select "PD3" from the variant component stimation and "Optimum" for compression.

Click the Launch Analysis button

Using FaST LMM

Step 1: Run a mixed model with FaST LMM

The genotype data for this exercise is located under

'Community Data'->iplant_training->advanced_gwas->fastlmm->input

Locate the FaST LMM App under

Public Apps->QTL and GWAS->Models and Workflows

In the Input Files section, click the "Browse" button next to the box labeled "Folder containing all input files". Navigate and select the input folder.

Type "MTDRY" in the box labeled "Base name for PLINK's .map and .ped files"

Filled launch window

In the section named General Options, change the value in the "Identifier for missing phenotype values" box from "-9" to "0".

Click the Launch Analysis button.

Step 2: Plot the results

Locate the application "Fast LMM Results Plotter"
Click on the Browse button next to the box labeled "Select FastLMM output file" and locate the output folder of the FaST LMM analysis. Select the file named "output-main.txt"
Click the Launch Analysis button