CWAS-Plus installation

Requirements

For CWAS-Plus to run, the users need to (1) install conda and Ensembl Variant Effect Predictor (VEP) and (2) download a few databases for annotation.

1. Required installations

  • Conda: CWAS-Plus install packages using conda environment. Please install conda or mamba.

  • VEP: VEP is used for variant annotation. Please refer to the reference and install VEP.

2. VEP resources

  • Missense database: Missense database containing scores to classify damaging missense variants are required. In CWAS-Plus, MPC database is available. If users want to use other database, they can download their own database and customize the configuration.txt to use it.

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

  • loftee plugin: loftee will be used to classify protein-truncating variants. Be aware of which branch you are cloning.

    cd $HOME/.vep/Plugins
wget https://github.com/konradjk/loftee/archive/refs/tags/v1.0.4_GRCh38.tar.gz
tar -zxvf v1.0.4_GRCh38.tar.gz
mv loftee-1.0.4_GRCh38 loftee

  • gerp bigwig: This file will be used for loftee plugin.

    wget https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/gerp_conservation_scores.homo_sapiens.GRCh38.bw

  • Human ancestor fasta: This file will be used for loftee plugin.

    wget https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/human_ancestor.fa.gz
wget https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/human_ancestor.fa.gz.fai
wget https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/human_ancestor.fa.gz.gzi

  • Conservation file: This file will be used for loftee plugin.

    wget https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/loftee.sql.gz
gunzip -k loftee.sql.gz

Install CWAS-Plus

Users can instasll CWAS-Plus through pip or github. We recommend installing under a conda environment to avoid global installation.

  • pip

conda create -n cwas python=3.10 r-base=4.2.2
conda activate cwas
pip install cwas

  • Github

conda create -n cwas python=3.10 r-base=4.2.2
conda activate cwas
git clone https://github.com/joonan-lab/cwas.git
pip install cwas

The installation of R package glmnet is also required for risk score analysis.

To start CWAS-Plus, type the command below. This will create a workspace (.cwas) for CWAS-Plus in home directory. You can specify the directory that will be used as a working directory. As a default, $HOME/.cwas will be set. If you have a pre-installed VEP, this process will find it automatically and type it to the configuration file.

  • -w: Path to the CWAS working directory. All default CWAS processes will save their output here if no specific output directory is given. By default, the directory is set to $HOME/.cwas.

cwas start -w .cwas_wd