downstreamGWAS is a companion package to tidyGWAS. downstreamGWAS provides functions to run standardize genetic pipelines using summary statistics as input. External software is packaged through docker files available at dockerhub.
In addition to this, reference files needed for pipelines bundled into the containers are available through zenodo. Link TBD.
DownstreamGWAS utilises three factors to make genetic analysis much simplified:
- Harmonized GWAS format through tidyGWAS
- External software packaged into docker images, that can be run on HPCs with singularity/apptainer
- References files collected and available for download, with harmonized filepaths
remotes::install_github("ararder/downstreamGWAS")
devtools::install_github("ararder/downstreamGWAS")downstreamGWAS requires a filepaths.yml file to be created, and for you to add some information to it.
dir_to_store_yaml_in = "/nas/depts/007/sullilab/shared/gwas_sumstats"
setup_filepaths_yml(dir_to_store_yaml_in)
# get script to download singularity images
sif_script()