prstools

prstools is software to create Polygenic Risk Scores (PRS) directly from the commandline.

It makes PRS generation easier, compared to previous tools, by:

• Super fast reading and matching of sumstats (handles odd formats).
• Rapid creation of the model.
• Automatic generation of the PRS Prediction for target plink files.

All the above, for a real GWAS sumstat, within 30 minutes using only 1 command. Installation and running the demo example should not take more than 10 minutes.

Website: https://prstools.readthedocs.io/

Install

To install use the following command.

pip install -U --prefer-binary prstools

For it to work, you should have python3.8 or later installed (pip is included in python3.8+). If the command above does not work directly you can install using conda (or mamba if you have that) by running conda install "python>=3.9". For other install issues please check the install guide or send us a mail.

How to use

Immediately after installing prstools, it should be possible to download & run the demo example (~4mb), by pasting the following into the commandline:

# Makes 'example' dir with data in current path:
prstools downloadutil --pattern example --destdir ./; cd example

# Run the model with example data:
prstools prscs2 --ref ldref_1kg_pop --target target \
                --sst sumstats.tsv --n_gwas 2565 --out ./result 

This will run PRS-CS2 and make PRS prediction using example data. For a more comprehensive introduction and the best and fastest way to get a PRS for your case, try the Getting Started Tutorial.

Additionaly, prstools provides documentation through its command-line interface. Run prst to see the available commands, or prst prscs2 --help for options and copy-pastable examples. The same documention is available online too.

Tutorial + Video

For more information and a hands-on demonstration of what prstools can do, have a look at the Getting Started Tutorial. There is also a Video. The tutorial+video is a tiny bit older than the current prstools version, which has more functionality. You can load the tutorial in a free cloud instance by clicking here: .

Contact

For questions and support please send a mail (menno.j.witteveen@gmail.com).

We are actively developing prstools and feedback by mail or our feedback form (with 🏆 lottery) is much appreciated!