GWASpoly

This guide provides a step-by-step approach to conducting Genome-Wide Association Studies (GWAS) using the GWASpoly tool, making it accessible for users at various skill levels. It offers insights into selecting files, configuring analysis parameters, and interpreting results effectively, including QTL analysis and visualization options.

Alex Sandercock
24 steps
3 minutes

On the left hand side menu, select "GWASpoly".

On the left hand main menu, GWASPoly is highlighted

Just as in other processes, you will need to select the VCF and trait file.

Under Choose VCF file selection, "browse" is highlighted

Select trait file.

Under choose trait file, "browse" is highlighted

One the file is selected, click "open".

Select the species ploidy.

Select the base pair window (MB) and significance threshold.

Base pair window selection is highlighted

Select the trait.

Select trait options with petal width highlighted

Select any fixed effects and then select the number of CPU cores.\ Note that fixed effects does not have an asterisk next to it, so it is not a required field.

Fixed effects selection with sepal lenght highlighted

Select the number of CPU cores.

Number of CPU core selection slider highlighted

The yellow informational button contains example files as well as a GWAS job summary.

Yellow informational option is open and list available options to choose from including summary stats, informational references and example data files

Summary information example

When you are satisfied with your selections, click "run analysis".

You can now view your results in various plots ways in the middle of your screen.

View the various analysis options by clicking on the tab with the plot or QTL model name on it.

You may make a model selection under plot controls by clicking on the small arrow. This only changes which models are being displayed on the Manhattan Plot.

Model selection option with all highlighted

More GWAS models are evaluated for polyploid individuals.

Here is the QQ plot for all of the GWASpoly models evaluated.

QTL significant marker table. This lists all of the significant markers associated with your selected trait across all model.

In the "Filter QTL by LD window" selection, you can also adjust the slider at the bottom to adjust the base pair window and filter QTLs.

Slider to adjust base pair and filter QTLs highlighted

The table underneath then shows filtered QTLs.

You can also see the number of QTLs detected in the blue box on the upper right hand of the BIGapp screen.

In the Multiple QTL model tab, you can select a model. A multiple QTL model will then be performed using the GWASpoly package to estimate the variance explained be each filtered QTL.\ \ You can use the slider at the bottom of the table to pan and see more information.

Model selection window options highlighted

Using the red "save" button on the right hand side of the screen, you can select various options regarding the figures available in this GWASpoly BIGapp section and then save both the image and the file using the grey save buttons at the bottom.

Save image and save file options highlighted

Also under the yellow informational button, you can view results descriptions under the BIGapp in-app Help pages.

Under the yellow informational option, parameters is highlighted

Result description information for GWAS in the BIGapp Help pages.

Results description tab in the help pages is highlighted

You have completed this training module for GWASpoly in the BIGapp. Return to the main training page to learn more about other BIGapp features.