| Option | Default | Description |
| --moi | A | mode of inheritance: 'A', additive |
| --resampling | False | directly draw sample genotypes from given haplotype pools (sample genotypes will be simulated on the fly if haplotype pools are not avaliable) |
| --def_rare | 0.01 | definition of rare variants: variant having 'MAF ⇐ frequency' will be considered a 'rare' variant; the opposite set is considered 'common' |
| --def_neutral | None | annotation value cut-offs that defines a variant to be 'neutral' (e.g. synonymous, non-coding etc. that will not contribute to any phenotype); any variant with 'function_score' X falling in this range will be considered neutral |
| --def_protective | None | annotation value cut-offs that defines a variant to be 'protective' (i.e., decrease disease risk or decrease quantitative traits value); any variant with 'function_score' X falling in this range will be considered protective |
| -P/--proportion_detrimental | None | proportion of deleterious variants associated with the trait of interest, i.e., the random set of the rest (1 - p) x 100% deleterious variants are non-causal: they do not contribute to the phenotype in simulations yet will present as noise in analysis |
| -Q/--proportion_protective | None | proportion of protective variants associated with the trait of interest, i.e., the random set of the rest (1 - p) x 100% protective variants are non-causal: they do not contribute to the phenotype in simulations yet will present as noise in analysis |
| --sample_size | None | total sample size |
| --p1 | None | proportion of affected individuals , or individuals with high extreme QT values sampled from infinite population (default set to None, meaning to sample from finite population speficied by --sample_size option). |
| --def_valid_locus | None | upper and lower bounds of variant counts that defines if a locus is 'valid', i.e., locus having number of variants falling out of this range will be ignored from power calculation |
| --rare_only | False | remove from analysis common variant sites in the population, i.e., those in the haplotype pool having MAF > $def_rare |
| --missing_as_wt | False | label missing genotype calls as wildtype genotypes |
| --missing_low_maf | None | variant sites having population MAF < P are set to missing |
| --missing_sites | None | proportion of missing variant sites |
| --missing_sites_deleterious | None | proportion of missing deleterious sites |
| --missing_sites_protective | None | proportion of missing protective sites |
| --missing_sites_neutral | None | proportion of missing neutral sites |
| --missing_sites_synonymous | None | proportion of missing synonymous sites |
| --missing_calls | None | proportion of missing genotype calls |
| --missing_calls_deleterious | None | proportion of missing genotype calls at deleterious sites |
| --missing_calls_protective | None | proportion of missing genotype calls at protective sites |
| --missing_calls_neutral | None | proportion of missing genotype calls at neutral sites |
| --missing_calls_synonymous | None | proportion of missing genotype calls at synonymous sites |
| --error_calls | None | proportion of error genotype calls |
| --error_calls_deleterious | None | proportion of error genotype calls at deleterious sites |
| --error_calls_protective | None | proportion of error genotype calls at protective sites |
| --error_calls_neutral | None | proportion of error genotype calls at neutral sites |
| --error_calls_synonymous | None | proportion of error genotype calls at synonymous sites |
| --power | None | power for which total sample size is calculated (this option is mutually exclusive with option '-- sample_size') |
| -r/--replicates | 1 | number of replicates for power evaluation |
| --alpha | 0.05 | significance level at which power will be evaluated |
| -l/--limit | None | if specified, will limit calculations to the first N groups in data . |
| -o/--output | None | output filename |
| -t/--title | None | unique identifier of a single command run |
| -v/--verbosity | 2 | verbosity level: 0 for absolutely quiet, 1 for less verbose, 2 for verbose, 3 for more debug information |
| -s/--seed | 0 | seed for random number generator, 0 for random seed |
| -j/--jobs | 2 | number of CPUs to use when multiple replicates are required via '-r' option . |
| -m/--methods | None | Method of one or more association tests. Parameters for each method should be specified together as a quoted long argument (e.g. --methods 'm --alternative 2' 'm1 --permute 1000'), although the common method parameters can be specified separately, as long as they do not conflict with command arguments. (e.g. --methods m1 m2 -p 1000 is equivalent to --methods 'm1 -p 1000' 'm2 -p 1000'.). You can use command 'spower show tests' for a list of association tests, and 'spower show test TST' for details about a test. |
| --discard_samples | None | Discard samples that match specified conditions within each test group. Currently only expressions in the form of '%(NA)>p' is provided to remove samples that have more 100*p percent of missing values. |
| --discard_variants | None | Discard variant sites based on specified conditions within each test group. Currently only expressions in the form of '%(NA)>p' is provided to remove variant sites that have more than 100*p percent of missing genotypes. Note that this filter will be applied after '--discard_samples' is applied, if the latter also is specified. |
