A complete example

1. Installing

1. The instruction or installing the basci GUI version of PAGEANT is detailed in the Github main page. Taking Windows laptop as an example, one could click this link to download a zipped folder, unzip it, and then doulbe click the PAGEANT.exe file to launch the GUI interface.

2. The instruction for installing the command line version of PAGENTA is detailed in the Wiki page.

2. Navigation of the GUI interface

0. "I/O", for input and output specification

1. "QA/QC", for quality control and assurance of "personal genome" and "population genome reference"

2. "Qualitative", for specifying parameters to report Qualitative traits.

3. "Quantitiative", for specifying parameters to report Qualitative traits.

4. "Query DB", for specifying external databases to query.

5. "QR code", for specifying the list of SNPs to generate a QR code.

3. Process a real genome from 23&Me

1. Prepare the "personal genome" file

2. Do a test run to get familiar with PAGEANT, and generate a list of SNPs used for 2nd Q and 3rd Q.

3. Create a new "population genome reference" that includes all the SNPs extracted from above.

4. Add a new Qualitative trait (2nd Q)

5. Add a new Quantitative trait (3rd Q)

4. Results interpretation

• 1st Q, to make sure the quality of personal genome data.

• 2nd Q, to get further assured with genetic reporting, and hopefully also become fascinated.

• 3rd Q, to learn more on PRS, including the mathematics and the limitations.

• 4th Q, to explore further natural traits of interest, by plugging with external genetic databases.

• 5th Q, to extract and visualize the genetic ID in QR code.