SAIGE-BRUSH

THe SAIGE-Biobank Re-Usable SAIGE Helper software implmentation. Implementation of SAIGE GWAS software with modifications, scalability, and user-friendly implementation.

Dependencies

These are the required dependencies on the host system for which you will be running SAIGE-BRUSH:

• Singularity version >= 3.0
• Golang version >= go1.13.5 (officially test on go1.13.5 and go1.15.2)

Getting Started

1. Download the Singularity image:

   singularity pull library://tbrunetti/default/saige-brush:v039 
   

2. Clone this repository:

   git clone https://github.com/tbrunetti/SAIGE-BRUSH.git
   

3. Find the go executable and optionally you can add it to your path or move the exeutable to the desired run location. It is called saigeBrush:

   cd SAIGE-BRUSH/bin
   chmod u+x saigeBrush
   

4. The config file is located in the container directory and named configSAIGE.txt:

   cd SAIGE-BRUSH/container
   

5. After these steps you now have downloaded everything you need and you can follow the instructions in the SAIGE-BRUSH Docs to get started on your analysis!

Test Data

A small binary test data set is available in the git repo under test_env/test_data. This set can be run on a local computer/laptop and meant to illustrate proof of principle and that the pipeline properly works. It typically runs the full binary pipline - see here for example from beginning to end in about 5-10 minutes. This was tested on a Ubuntu 18.04LTS Linux OS laptop with 12 cores/threads. Memory footprint is very low, so a standard laptop should not run into any memory issues on the test set.

1. Make sure you have properly installed and met all the dependencies listed

2. Complete tasks (steps 1-3) in the Getting Started Section above

3. Navigate to the test_data directory:

   cd ../test_env/test_data
   

4. Open the file test_1k_configSAIGE.txt and replace all values where it requires /path/to/... with the full path location to the file listed for the paratmer. No need to change anything else in the config file, just the paths.

5. Run the pipeline!

   cd ../../bin/
   ./saigeBrush test_1k_configSAIGE.txt 1> myLog.log 2> myLog.err
   

6. It will create a full set of output for a small uninteresting random portion of chromosome 22. For more information on expected output and how to run the test data, visit the test data section of our documentation. Here is an image of the what the test data GWAS images generated from the pipeline should look like. The pdf file and associated images will be located in test_1k_finalResults/association_analysis_results/:

Full Documentation

Please visit the SAIGE-BRUSH Docs for detailed information on getting started and running the framework.