Getting started¶

Quick start¶

To run GWA-X, use the command main.py, followed by options and flags as needed:

python main.py \
    --bed hapnest_file \
    --phenoFile pheno1.phen \
    --bsize 5000 \
    --mperm 1000 \
    --out test

For more examples of running GWA-X, see the examples page.

You also can get a full list of options by using python main.py --help

Option	Argument	Required	Description
--bed, --pgen	FILE	Required	Either bed/bim/fam prefix that assumes file.bed, file.bim, file.fam exist, or pgen/pvar/psam prefix that assumes file.pgen, file.pvar, file.psam exist. DO NOT include the file extension
--phenoFile	FILE	Required	Phenotypes file in whitespace-delimited format. If it contains multiple columns, only the first column or --phenoCol will be used
--bsize	INT	Required	Size of genotype blocks loaded at one time. Adjust according to GPU memory size (5000 is recommended as starting point)
--mperm	INT	Optional	Number of permutations for max(T). 0 means GWAS without permutation tests
--covarFile	FILE	Optional	Covariates file in whitespace-delimited format
--phenoCol	STRING	Optional	The column name of phenotype to use for analysis
--regenie-pred	FILE	Optional	File containing LOCO predictions from REGENIE's step 1
--snp-from	STRING	Optional	Exclude all variants with smaller position values than this variant ID
--snp-to	STRING	Optional	Exclude all variants with higher position values than this variant ID

Option	Argument	Required	Description
--out	FILE PREFIX	Required	Prefix for output files' name

Option	Argument	Required	Description
--co2	FLAG	Optional	Track energy and CO2 used during analysis
--gpu-ids	LIST	Optional	The GPU device IDs to use (comma-separated list). Unset it to use available GPUs