Step 2: test genetic variants

Step 2 uses the Step 1 null model and variance ratios to test variants in a specified genomic region.

The tested simulated-data command is available in the Step 2 tabs on the CASTIE home page for both container and Pixi installations.

Important inputs:

• --bedFile, --bimFile, and --famFile: association-test PLINK files
• --GMMATmodelFile: Step 1 .rda model
• --varianceRatioFile: Step 1 variance-ratio file
• --rangestoIncludeFile: chromosome, start, and end interval
• --SAIGEOutputFile: output path for variant-level results
• --output_format: output format, default = parquet, can switch to txt
• --minMAF=0.05: please set for common variants only
• --pval_cutoff_for_gxe: main-effect p-value cutoff for running GxC tests, default = 1 (testing all)

Main-effect results use BETA, SE, and p.value. Dynamic interaction results are in columns*_ge, comma separated, following the order of --dynamicCovarColList supplied in Step 1.