Fine-mapping with infinitesimal effects v1.2

This repo contains code for SuSiE-inf (v1.4) and FINEMAP-inf (v1.3)

Getting started

Python3.9 is recommended

Clone this repo:

git clone https://github.com/FinucaneLab/fine-mapping-inf.git
cd fine-mapping-inf

Install dependencies:

setuptools
wheel
numpy
pandas
scipy
bgzip

We recommend that you install both SuSiE-inf and FINEMAP-inf.

To install SuSiE-inf:

cd susieinf
python setup.py bdist_wheel
pip install .

Similarly, to install FINEMAP-inf:

cd finemapinf
python setup.py bdist_wheel
pip install .

Once completed, run

python run_fine_mapping.py -h

to print a list of all command-line options.

Tutorial

Please see wiki for tutorial. Note that both SuSiE-inf and FINEMAP-inf are developed for use in single-cohort fine-mapping with in-sample LD, for fine-mapping of meta-analyzed GWAS with reference panel LD, please see methods like SLALOM or CARMA.

Authors

Ran Cui Zhou Fan

Contact

For questions and comments, please contact Ran Cui at rancui@broadinstitute.org