This repo contains code for SuSiE-inf (v1.4) and FINEMAP-inf (v1.3)
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.
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.
Ran Cui Zhou Fan
For questions and comments, please contact Ran Cui at rancui@broadinstitute.org