mlm_analysis_pipeline

This is a nextflow pipeline that performs mixed model association analysis using SAIGE

Obtaining the pipeline

The pipeline can be cloned from git using the following command:

    git clone https://github.com/BioPsyk/mlm_analysis_pipeline.git

Usage

The pipeline can be launched from your working directory using the following command:

    nextflow run main.nf \
    --bfile <path to pruned plink files for making the GRM in step 1 of SAIGE> \
    --genotypes <path to json file containing per chromosome VCF.gz files> \
    --phenoCovFile <path to file containing the phenotype and covariates> \
    --outcome <binary/continuous> \
    --phenotype <phenotype col name in the supplied phenoCovFile> \
    --covariates <comma separated list of covariates to include in the model>
    -w <path to where you want the nextflow work directory to be present>

Running nextflow run main.nf -h displays the help message

The default values for all parameters and example file formats can be seen from the
config file: nextlow.config

I recommend making changes here for project name on slurm etc before running the pipeline.

Helpful tip

Nextflow recommends not launching more than one workflow from the same directory.
So if you are launching the pipeline on multiple phenotypes or datasets, create new
directories and use --chdir option in the sbatch command to specify a launch directory

Expected outputs

• Per chromosome GWAS association outputs
• Concatenated GWAS association output
• Manhattan and qq plots

Bugs and error reporting

Any questions or concerns regarding the pipeline, raise an issue on github (or) send me an e-mail/slack message [email protected]