omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
96 stars 22 forks source link

Add option to save FINEMAP files to a specific output directory #61

Closed jdblischak closed 3 years ago

jdblischak commented 3 years ago

It can be useful to save the FINEMAP output files for later inspection. This PR adds the flag --finemap-dir to specify the output directory instead of using a temporary one.

Example usage:

python finemapper.py \
    --geno example_data/chr1 \
    --sumstats example_data/chr1.finemap_sumstats.txt.gz \
    --n 383290 \
    --chr 1 \
    --start 46000001 \
    --end 49000001 \
    --method finemap \
    --finemap-exe <path to FINEMAP v1.4 executable> \
    --max-num-causal 5 \
    --cache-dir LD_cache \
    --out output/finemap.finemap_exe.1.46000001.49000001.gz \
    --finemap-dir output/finemap.finemap_exe.1.46000001.49000001
omerwe commented 3 years ago

This is awesome, thanks!