Command-line reference

After installation (see Installation), all functionality is available through the posthoc command:

posthoc --help
posthoc <command> --help

posthoc

Usage

posthoc [OPTIONS] COMMAND [ARGS]...

Options

--verbose: Enable debug logging.

The top-level --verbose flag enables debug-level logging for any subcommand; place it before the subcommand name, e.g. posthoc --verbose attribute ....

Every subcommand that reads real genotype data (baseline, attribute, pal) shares the same --pfile/--pheno/--pheno-name/--covar and QC options (--maf, --geno, --indep-pairwise) — see Input data formats for what those expect and how samples are aligned.

Commands