PolygenicRiskScores.jl (previously PRS.jl)

PolygenicRiskScores.jl is a port of PRS-CS to Julia.

Usage

Using the test data from PRS-CS at ~/prs-data, the following invocation should work when run in the root directory of PolygenicRiskScores.jl:

julia --project -e "using PolygenicRiskScores; PolygenicRiskScores.main()" -- --ref_dir=~/prs-data/ldblk_1kg_eur --bim_prefix=~/prs-data/test --sst_file=~/prs-data/sumstats.txt --n_gwas=200000 --chrom=22 --phi=1e-2 --n_iter=1000 --out_dir=~/prs-data/output_jl

Multi-threaded CSV reading

Julia's CSV reader supports multi-threaded CSV reading. In order to enable this, we need to load Julia with more than one thread. This is done through the JULIA_NUM_THREADS environment variable:

JULIA_NUM_THREADS=8 julia --project -e "using PolygenicRiskScores; PolygenicRiskScores.main()" ...

The above code would run PolygenicRiskScores.jl with 8 threads.