Testing Imputationserver PGS: Step by Step

To test Imputationserver PGS, please execute the following steps:

0. Signup and create a login:

Imputationserver PGS requires a login to access the Polygenic Risk Score (PGS) calculation service. This login is crucial to maintain the security and privacy of any uploaded human genotype data.

Users have the flexibility to create this login either with or without providing an email address. Please visit the signup page and proceed to create a login.

1. Download the Example Dataset: Start by downloading the example dataset provided for testing the PGS extension. You can obtain the dataset by clicking on the following link: 50-samples.zip.

2. Unpack the Data: After downloading the zip file, unzip or extract its contents to a location of your choice on your computer.

3. Access Polygenic Risk Score Application: Navigate to the "Run" menu and select "Polygenic Risk Score" from the options.

4. Choose 1000 Genomes Phase 3 Panel: In the Polygenic Risk Score application, select the "1000 Genomes Phase 3" panel as the reference dataset for imputation.

5. Specify PGS Catalog and Trait: Identify and specify the Polygenic Score (PGS) Catalog you want to use for scoring. Choose a relevant trait for the analysis, such as "Cancer".

6. Optional Ancestry Estimation: Optionally, you can choose to include ancestry estimation in your analysis. This step may enhance the precision and interpreation of the results.

7. Agree to Terms of Service: Before proceeding, make sure to read and agree to the Terms of Service provided by Imputationserver. It is essential to comply with the platform's terms and conditions.

8. Submit the Job: After configuring all the necessary parameters, click on the "Submit" button to initiate the PGS calculation.

9. Monitor Progress: Depending on the server load, the calculation may take a certain amount of time (about 30 minutes). Allow the process to complete.

10. Download Results: Once the calculation is finished, you can view the results provided by Imputationserver PGS and download a report and all calcuated scores.

Congratulations! You have successfully tested Imputationserver PGS using the provided example dataset and configuration settings. Now you are ready to use the service with yout own dataset!