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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:

Software Requirements:

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.