Clumping GWAS files and performing LDSC

Clone repo & submodules

git clone --recurse-submodules https://github.com/MRCIEU/gwas_processing
cd gwas_processing

Docker

To create the container:

docker build -t gwas_processing .
docker rm -f gwas_processing
docker run -d --name gwas_processing -v /path/to/data:/data gwas_processing 

To perform clumping:

docker run -v /path/to/data:/data gwas_processing clump.py --bcf /data/path/to/data.vcf.gz --out /data/path/to/clump.txt

To perform LD score regression:

docker run -v /path/to/data:/data gwas_processing ldsc.py --bcf /data/path/to/data.vcf.gz --out /data/path/to/ldsc.txt

BC4

module load languages/anaconda3/2018.12
virtualenv venv
source ./venv/bin/activate
python clump.py -h
python ldsc.py -h

Reference data

The /data directory linked in the docker run commands above should have a directory called ref containing LD score files and an LD reference panel e.g.

Get LD score files

curl -SL https://data.broadinstitute.org/alkesgroup/LDSCORE/eur_w_ld_chr.tar.bz2 | tar -xvjC /data/ref
cp ../gwas_processing/w_hm3.noMHC.snplist.gz /data/bgc/temp/snplist.gz

Get LD reference panel

curl -SL https://www.dropbox.com/s/yuo7htp80hizigy/ | tar -xzvC /data/ref