JamesYang007 / ghostbasil

GhostKnockoff + BASIL

GhostBASIL

This is a repository for experimental code using GhostKnockoff and BASIL framework for fast and efficient LASSO fitting on high-dimensional data. Specifically, this library is created with the intention of applying it on GWAS summary statistics.

Dependencies

• Bazel

Developer Installation

Run the following command to generate machine-specific .bazelrc:

./generate_bazelrc

Then, install the developement dependencies:

mamba update -y conda
mamba env create
conda activate ghostbasil

Our tools require omp to be installed on the system. On Mac, it must be installed with Homebrew as our build system assumes:

brew install libomp

See the following for installations of each of the sub-packages:

• R README
• C++ README

References

• Summary statistics knockoff inference empowers identification of putative causal variants in genome-wide association studies
• A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank