• This repository gives you default datasets and configuration files to execute Category-Wide Assiciation Study (CWAS-Plus).
• You can reproduce the results of An et al., 2018 by using these datasets.

• annotation_keys.yaml: List of annotation datasets with the exact file names and short names used for CWAS-Plus annotation.
• gene_matrix.txt: List of genes with their functional annotations.
• download_vep_resources.sh: Code to download VEP resources.
• configuration.txt: Configuration file for CWAS-Plus specifying VEP path and required resources.
• functional_annotations.tar.gz: BED files for annotating variants. After decompressing, please move the files within the directory to the parent directory "cwas-dataset."
• MPC_hg38.vcf.bgz: Database for annotation damaging missense variants. For further information, please refer to the provided reference.
• BED files for vertebrate conservation scores
  • PhyloP46way and PhastCons46Way
  • Due to the large file sizes, we provide an alternative download link for the original files.

git clone https://github.com/joonan-lab/cwas-dataset.git
cd cwas-dataset
git lfs pull

To download VEP resources all at once, use the following command.

sh download_vep_resources.sh

If it asks for permission, try sh download_vep_resources.sh.

• All the analyses in CWAS were based on hg38, so all the BED and BigWig files in this repository were also for hg38.
• You must match the genome assembly between datasets (especially VCF, BED, and BigWig files) for CWAS-Plus.