SAIGE

SAIGE is an R package developed with Rcpp for genome-wide association tests in large-scale data sets and biobanks.

For more information: https://saigegit.github.io/SAIGE-doc/
Source code: https://github.com/saigegit/SAIGE

Running SAIGE on Comet

We have installed SAIGE on Comet using the images published on Docker Hub.

The SAIGE container is stored in the /nobackup/shared/containers directory and is accessible to all users of Comet. You do not need to take a copy of the container file; it should be left in its original location.

You can find the container files here:

/nobackup/shared/containers/saige-1.5.1.sif

We normally recommend using the latest version of the container, in the case of SAIGE, the version numbers represent the version of the SAIGE software itself.

Container Image Versions

We may reference a specific container file, such as saige-1.5.1, but you should always check whether this is the most recent version of the container available. Simply ls the /nobackup/shared/containers directory and you will be able to see if there are any newer versions listed.

We have provided a convenience script that will automate all of steps needed to run applications inside the container, as well as access your $HOME, /scratch and /nobackup directories to just two simple commands.

/nobackup/shared/containers/saige-1.5.1.sh

There is a corresponding .sh script for each version of the container image we make available.

Just source this file and it will take care of loading apptainer, setting up your bind directories and calling the exec command for you - and give you a single command called container.run (instead of the really long apptainer exec command) to then run anything you want inside the container.

Simple use of SAIGE

All of the SAIGE commands are installed under /usr/local/bin within the container, but can be called by simply using the container.run command. You do not need to give their full path details and you do not need to prefix them with Rscript.

Commands available:

createSparseGRM.R
step1_fitNULLGLMM.R
step2_SPAtests.R
step3_LDmat.R

For example, to see the help page for the step1_fitNULLGLMM.R command, run as follows:

$ source /nobackup/shared/containers/saige-1.5.1.sh
$ container.run step1_fitNULLGLMM --help
R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Usage: /usr/local/bin/step1_fitNULLGLMM.R [options]

Options:
	--plinkFile=PLINKFILE
		Path to plink file for creating the genetic relationship matrix (GRM). minMAFforGRM can be used to specify the minimum MAF and maxMissingRate can be used to specify the maximum missing rates  of markers in the plink file to be used for constructing GRM. Genetic markers are also randomly selected from the plink file to estimate the variance ratios

	--bedFile=BEDFILE
		Path to bed file. If plinkFile is specified, 'plinkFile'.bed will be used

	--bimFile=BIMFILE
		Path to bim file. If plinkFile is specified, 'plinkFile'.bim will be used

	--famFile=FAMFILE
		Path to fam file. If plinkFile is specified, 'plinkFile'.fam will be used
...
$

Further documentation: https://saigegit.github.io/SAIGE-doc/

Running the SAIGE Examples

The Single-variant test example from the SAIGE website can be run with the container as follows:

$ source /nobackup/shared/containers/saige-1.5.1.sh
$ container.run step1_fitNULLGLMM.R     \
        --plinkFile=/app/extdata/input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly_22chr  \
        --phenoFile=/app/extdata/input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt \
        --phenoCol=y_binary \
        --covarColList=x1,x2 \
        --qCovarColList=x2  \
        --sampleIDColinphenoFile=IID \
        --traitType=binary        \
        --outputPrefix=./example_binary \
        --nThreads=4 \
        --IsOverwriteVarianceRatioFile=TRUE
$

Note:

Sample data - (plinkFile and phenoFile) The sample data noted in the example is available under /app/extdata within the container. Adjust any paths using this data in the online guide to use /app/extdata instead.
Threads - Set the nThreads value to the number of cores you have requested via Slurm.

Single-variant example: https://saigegit.github.io/SAIGE-doc/docs/single_step1.html

Accessing Data

As long as you use the container.run method to launch the applications, you will automatically be able to read and write to files in the three main user areas of Comet: $HOME, /scratch and /nobackup directories.

If you run any of the applications inside the container manually, without using the container.run helper you will need to use the –bind argument to apptainer to ensure that all relevant directories are exposed within the container.

Do remember that the container filesystem itself cannot be changed - so you won't be able to write or update to /usr/local, /opt, /etc, /app or any other internal folders - keep output directories restricted to the three areas listed above.

Installing SAIGE on Comet

Important!

This section is only intended for RSE HPC admin staff or users who are interested in how SAIGE is installed. If you just need to use SAIGE, then stop reading here.

Installing

#!/bin/bash
module load apptainer
export APPTAINER_TMPDIR=/scratch
apptainer build saige-1.5.1.sif docker://wzhou88/saige:1.5.1

Container definition

This has no container definition, as we are simply translating the published Saige container from Docker hub to a local Apptainer format.

Helper script

#!/bin/bash
module load apptainer
IMAGE_NAME=/nobackup/shared/containers/saige-1.5.1.sif

container.run() {
    # Run a command inside the container...
    # automatically bind the /scratch and /nobackup dirs
    # pass through any additional parameters given on the command line
    apptainer exec --bind /scratch:/scratch --bind /nobackup:/nobackup ${IMAGE_NAME} $@
}

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