Documentation for SAIGE Pipelines

Overview

SAIGE is a popular tool for performing association tests with multiple types of genetic data, such as:

• Common Variants
• Rare Variants
• Gene Burden

Here are some SAIGE-specific resources:

• Original SAIGE Paper for Your Reference
• SAIGE-GENE Paper for Your Reference
• SAIGE Documentation

Software Requirements:

• git
• Some text editor for updating the nextflow.config profiles such as vim or nano
• Nextflow version 23.04.1.5866
• Singularity version 3.8.3 OR Docker version 4.30.0
• JDK version 11.0.5

Steps for Runnning One of the Pipelines with Test Data

Note: test data were obtained from the SAIGE github repo.

Steps:

1. Start your own project directory and go there
   • mkdir my_new_saige_project
   • cd my_new_saige_project
2. Build the saige.sif singularity image
   • singularity build saige.sif docker://pennbiobank/saige:latest
   • you do not necessarily have to do this repeatedly, BUT it's good for versioning to keep it with the project
   • if you want to reuse containers, you could build containers in a more general containers directory somewhere
3. Download the source code by cloning from git
   • git clone https://github.com/PMBB-Informatics-and-Genomics/pmbb-nf-toolkit-saige-family.git
   • You may do this in your project directory, but it often makes sense to clone into a general tools location
4. Copy the contents of one of the test data directories
   • cp -r pmbb-nf-toolkit-saige-family/test_data/ExWAS/test_config_exwas_no_GRM/* .
5. Fill out the nextflow.config file to make sure it matches your system
   • See nextflow executor information here.
   • From the command line, you can use the text editor vim with vim nextflow.config
   • The profile's attribute process.container should be set to '/path/to/saige.sif' (replace /path/to with the location where you built the image in step 2)
6. Do a stub run to test
   • nextflow run /path/to/pmbb-nf-toolkit-saige-family/workflows/saige_exwas.nf -profile cluster -stub
   • Note: Replace /path/to/ with the actual path (full or relative) where you cloned the repository in step 3.
   • ^ make sure you select the correct profile you set up
7. Now run the workflow on the actual data!
   • nextflow run /path/to/pmbb-nf-toolkit-saige-family/workflows/saige_exwas.nf -profile cluster
   • Note: Replace /path/to/ with the actual path (full or relative) where you cloned the repository in step 3.

Steps for Runnning One of the Pipelines with YOUR Data

Steps:

1. Start your own project directory and go there
   • mkdir my_new_saige_project
   • cd my_new_saige_project
2. Build the saige.sif singularity image
   • singularity build saige.sif docker://pennbiobank/saige:latest
   • you do not necessarily have to do this repeatedly, BUT it can be good for versioning to keep it with the project in case it gets updated later
   • if you want to reuse containers, you could build containers in a more general containers directory somewhere
3. Download the source code by cloning from git
   • git clone https://github.com/PMBB-Informatics-and-Genomics/pmbb-nf-toolkit-saige-family.git
   • You may do this in your project directory, but it often makes sense to clone into a general tools location
4. Set up the appropriate config file for the pipeline you want to run
   • Update any and all input files!
   • Double-check parameters for running the software (QC filters, settings, etc)
   • Refer to the READMEs directory with more info for every parameter and input file
5. Fill out the nextflow.config file to make sure it matches your system
   • See nextflow executor information here.
   • From the command line, you can use the text editor vim with vim nextflow.config
   • The profile's attribute process.container should be set to '/path/to/saige.sif' (replace /path/to/ with the path where you built the image in step 2)
   • Make sure the nextflow.config file has an includeConfig statement
6. Do a stub run to test
   • nextflow run /path/to/pmbb-nf-toolkit-saige-family/workflows/saige_exwas.nf -profile cluster -stub
   • Note: Replace /path/to/ with the actual path (full or relative) where you cloned the repository in step 3.
   • ^ make sure you select the correct profile you set up
7. Now run the workflow on the actual data!
   • nextflow run /path/to/pmbb-nf-toolkit-saige-family/workflows/saige_exwas.nf -profile cluster
   • Note: Replace /path/to/ with the actual path (full or relative) where you cloned the repository in step 3.

Notes to keep in mind when applying this process to your data:

• You do not need to copy YOUR data to the Input/ folder (unless you want to). It usually makes sense to add full paths to your configs/workflow_specific_config as needed.