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Interactive notebook for quality control and Spark-based genome wide association analysis using HAIL and VariantSpark.
Jupyter Notebook HTML Shell
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README.md

ViGWAS: automation and visualization for population-scale association studies

This package implements most of Hail v0.2 feature in a Jupyter notebook. It reports the result in a well-formatted HTML file.

*** The HTML report can be only viewed using the Firefox browser.

Installation

To run ViGWAS on AWS or VirtualBox please look at the instructions in the "Instructions" folder.

The VirtualBox image (~7GB) is available here.

To install ViGWAS on your computer you may follow the instruction provided in "ViGWAS_Setup_Instruction.sh".

To install and run ViGWAS on a cluster you may need to modify the installation procedure. We have not provided the guidelines for that setup yet.

Usage

Please refer to "UserManual.pdf"

Example data

A set of example tiny datasets are provided in the "sample_input" folder.

An example HTML output is available in "ExampleReport" folder. Download the folder and open any of the HTML files using Firefox browser (ONLY Firefox browser). You can navigate the report using the top bar menu in the HTML report.

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