3. Dependencies

In order to run SAFFARI you need to install the following dependencies prior to the workflow execution:

Polyfun

git clone https://github.com/omerwe/polyfun
cd polyfun
conda env create -f polyfun.yml
conda activate polyfun

FINEMAP

wget http://www.christianbenner.com/finemap_v1.4.2_x86_64.tgz
tar -xvzf finemap_v1.4.2_x86_64.tgz

SuSiE

conda install conda-forge::r-susier

Snakemake

conda create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

Precomputed UKB LD matrices

LD matrices generate by Alkes Price group can be downloaded from an Amazon S3 bucket via the AWS CLI.

conda install awscli # if not installed
mkdir UKBB_LD
aws s3 cp --no-sign-request  s3://broad-alkesgroup-ukbb-ld/UKBB_LD/ UKBB_LD --recursive

Annotations (baseline LF2.2 model)

For estimating the functional priors

mkdir UKBB_priors
mv UKBB_LD/baselineLF_v2.2.UKB.polyfun.tar.gz UKBB_priors
tar -xvzf UKBB_priors/baselineLF_v2.2.UKB.polyfun.tar.gz