jielab/penguin

PENGUIN: Progressively Establish Novel Genetics Underlying Interrelation

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.

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

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

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

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

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Contact & Cite

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