Genomic Prediction

This guide provides a comprehensive overview of the Genomic Prediction feature in the BIGapp, enabling users to effectively analyze genetic data. By following the outlined steps, users can upload relevant files, select traits, and run analyses to obtain predicted phenotypes and estimated breeding values. Additionally, the guide highlights advanced options and resources for further exploration, making it a valuable tool for anyone looking to enhance their understanding of genomic prediction.

Alex Sandercock
23 steps
2 minutes

Here, a users can predict trait information and Estimated-Breeding-Values (EBVs) for provided samples.\ \ There are two options to do so: 1. Provide a single VCF file, where predictions will be made for all individuals (both w/ and w/out trait information). The output tables will annotate which samples had trait information provided. 2. The user provides one VCF file of sample data to train the model, and a second VCF file to predict trait and EBV information for. This can be selected in the "Advanced Options"

On the left hand side menu, choose "genomic prediction".

On the left hand menu genomic prediction option is highlighted

Click on "browse" to select the VCF file.

Under Choose VCF file, "browse" is highlighted

Select your file and click on "open".

Click on "browse" and select the trait file.

Under choose trait file, "browse" is highlighted

Select your file and click on "open".

Select the species ploidy.

Species ploidy level selection highlighted

Select the traits you wish to analyze. You can choose more than one.

Under select traits, options with sepal width highlighted

You can also select fixed effects.\ Please note that this is a beta feature.

Select Fixed effects highlighted. This is a beta feature.

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

Click "proceed".

Here you can view the Predicted Pheno Table as well as the EBVs table with your data.

You can see more of your data by using the slider feature at the bottom of the table.

To access the EBV table, click on the tab with that title.

You may also view advanced options for analysis. Please note that this is a beta feature.

Click on "advanced options (beta).

Advanced options (beta) button highlighted

Within the beta feature "Advanced Options", select "browse" to choose the prediction VCF file. \ \ This allows the option to input a second VCF file of samples with unknown trait information. The samples from the first VCF with trait information will then be used to train the model and predict trait and EBV information only for the samples in the second VCF file.

Under advance options, choose prediction VCF browse highlighted

Select your file and click "open".

Once the upload is complete, you can choose to save.

Run your analysis by clicking on the "run analysis" button.

Click "proceed".

You can then view your results.

Results from running analysis highlighted

To save results, click on the red "save" button the right hand side of your screen under "plot controls".

Summary and example files are also located within the yellow "i" button near "run analysis".

Summary button with summary file, help page links and example files

Here you can view the BIGapp Selection Summary. You can choose to download the summary if you wish.

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

Genomic Prediction

Alex Sandercock
23 steps
2 minutes

On the left hand side menu, choose "genomic prediction".

Click on "browse" to select the VCF file.

Select your file and click on "open".

Click on "browse" and select the trait file.

Select your file and click on "open".

Select the species ploidy.

Select the traits you wish to analyze. You can choose more than one.

You can also select fixed effects.\ Please note that this is a beta feature.

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

Click "proceed".

Here you can view the Predicted Pheno Table as well as the EBVs table with your data.

You can see more of your data by using the slider feature at the bottom of the table.

To access the EBV table, click on the tab with that title.

You may also view advanced options for analysis. Please note that this is a beta feature.

Click on "advanced options (beta).

Select your file and click "open".

Once the upload is complete, you can choose to save.

Run your analysis by clicking on the "run analysis" button.

Click "proceed".

You can then view your results.

To save results, click on the red "save" button the right hand side of your screen under "plot controls".

Summary and example files are also located within the yellow "i" button near "run analysis".

Here you can view the BIGapp Selection Summary. You can choose to download the summary if you wish.

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