pgscalculator

This workflow aims to run different PGS methods using cleansumstats output so the result is comparable.

Created by Jesper R. Gådin and Andrew Schork

Quick start

Make sure git and singularity (or docker) are installed. Then clone the code from github. ```

Are the required software available

singularity --version docker --version git --version

Clone and enter the pgscalculator github project

git clone https://github.com/BioPsyk/pgscalculator.git cd pgscalculator ```

Singularity

Using singularity (use path to image). Run using an example file for a random subset of variants on all chromosomes. Just replace the input in -i with a folder cleaned by cleansumstats.

```bash

pull singularity image returning the image as a file (<1GB)

mkdir -p sif singularity pull sif/ibp-pgscalculator-base_version-0.6.0.sif docker://biopsyk/ibp-pgscalculator:0.6.0-amd64

Note: For ARM64 systems (e.g., Apple Silicon Macs), append -arm64 to the version tag instead of -amd64. For example: 1.3.0-arm64.

Run both calc posterior and score in one run

./pgscalculator.sh \ -j sif/ibp-pgscalculator-baseversion-0.5.4.sif \ -i tests/exampledata/sumstats/sumstat2 \ -l references/ld-sbayesr/ukb/bandukb10khm3 \ -g references/genotypestest/plink \ -f references/genotypestest/mapfiles/plinkgenodirgenofiles.txt \ -c conf/sbayesr.config \ -o outtest1

```

Change config to prscs method ```

Run both calc posterior and score in one run

./pgscalculator.sh \ -j sif/ibp-pgscalculator-baseversion-0.5.4.sif \ -i tests/exampledata/sumstats/sumstat2 \ -l references/ld-prscs/ldblk1kgeur \ -g references/genotypestest/plink \ -f references/genotypestest/mapfiles/plinkgenodirgenofiles.txt \ -c conf/prscs.config \ -o outtest_2

```

Specifying Resources

It is possible to run both interactive and batch jobs. Below is an example on GDK(HPC) starting an interactive node. Jobs require at minimum 6 cpus and 10g, but prefereably 22 cpus and 20g srun --mem=10g --ntasks 1 --cpus-per-task 6 --time=1:00:00 --account ibp_pipeline_cleansumstats --pty /bin/bash srun --mem=20g --ntasks 1 --cpus-per-task 22 --time=1:00:00 --account ibp_pipeline_cleansumstats --pty /bin/bash

More documentation

• See SNP inclusion list
• See Two step analysis
• See Use Docker
• See FAQ