/penguin

PENGUIN: Progressively Establish Novel Genetics Underlying Interrelation

GNU General Public License v3.0GPL-3.0

PENGUIN: Progressively Establish Novel Genetics Underlying Interrelation


1. Download & Run

  1. Download executables for Linux, Mac OS
  2. For Mac-OS: follow the instruction to install Homebrew and then run "brew install zbar llvm", to install necessary libraries, and then double click "PENGUIN".
  • For Linux: run "sudo apt-get install libzbar0 python3-pyqt5" to install packages, then run PAGEANT by typing "./PENGUIN".
  • 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.

  • C1 (Crossing): cross GWAS QC (comparing EAF and BETA), and cross-trait meta-analyses.

  • C1

  • C2 (Correlation): using methods such as LDSC to calculate genetic correlation.

  • C2

  • C3 (Causation): using Mendelian Randomization to assess causality

  • C3

  • C4 (Colocalization): for pleiotropic loci of interest, finding causal variants and mechanisms

  • C4

  • C5: Collaboration: finding common pathways and networks, implicating potential drug targets

  • C5

Contact & Cite

  • Jie Huang MD MPH PhD, Department of Global Health, Peking University School of Public Health
  • Manuscript under review