PAGEANT: Personal Access to Genome & Analysis of Natural Traits

1. Download & Run

1. Download executables for Windows, Linux, Mac OS
2. For Windows OS: the program could be run directly by double clicking "PAGEANT.exe".
3. For Mac-OS: follow the instruction to install Homebrew and then run "brew install zbar llvm", to install necessary libraries, and then double click "PAGEANT".

• For Linux: run "sudo apt-get install libzbar0 python3-pyqt5" to install packages, then run PAGEANT by typing "./PAGEANT".
• For advanced users, please check out the wiki for command line approaches.

2. Example test-run

Once the GUI window is displayed, a user simply needs to click the “Analyze” button to do a “test-drive” without doing anything else. Once a user gets familiar with the test-drive, he/she could change all parameters in the GUI interface:

• sample name
• genotype data (in VCF format)
• configuration file
• output location for the genetic report and log file

3. Example report

• A full example genetic report can be viewed here.

• Q1：Displayings user's PCA and UMAP among population reference

• Q2: Qualitative traits report

• Q3: Quantitative traits reportaa

• Q4: Query ClinVAR database

• Q5: QR code to extract genetic data

Contact & Cite

• Jie Huang MD MPH PhD, Southern University of Science and Technology
• Jie Huang, Zhi-Sheng Liang, Stefano Pallotti, Janice M. Ranson, David J. Llewellyn, Zhi-Jie Zheng, Dan A. King, Qiang Zhou, Houfeng Zheng, Valerio Napolioni. PAGEANT: personal access to genome and analysis of natural traits. Nucleic Acids Res. 2022 Apr 22;50(7):e39.