Table of Command Options

Common options

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.

LOGIT model options

Option Default Description
-a/--OR_rare_detrimental 1.0 odds ratio for detrimental rare variants
-b/--OR_rare_protective 1.0 odds ratio for protective rare variants
-A/--ORmax_rare_detrimental None maximum odds ratio for detrimental rare variants, applicable to variable effects model
-B/--ORmin_rare_protective None minimum odds ratio for protective rare variants, applicable to variable effects model
-c/--OR_common_detrimental 1.0 odds ratio for detrimental common variants
-d/--OR_common_protective 1.0 odds ratio for protective common variants
-f/--baseline_effect 0.01 penetrance of wildtype genotypes

PAR model options

Option Default Description
-a/--PAR_rare_detrimental 0.0 Population attributable risk for detrimental rare variants
-b/--PAR_rare_protective 0.0 Population attributable risk for protective rare variants
-c/--PAR_common_detrimental 0.0 Population attributable risk for detrimental common variants
-d/--PAR_common_protective 0.0 Population attributable risk for protective common variants
--PAR_variable False use variable population attributable risks: the smaller the MAF the larger the PAR
-f/--baseline_effect 0.01 penetrance of wildtype genotypes

LNR model options

Option Default Description
-a/--meanshift_rare_detrimental 0.0 mean shift in quantitative value w.r.t standard deviation due to detrimental rare variants i.e., by 'MULTIPLIER * sigma'
-b/--meanshift_rare_protective 0.0 mean shift in quantitative value w.r.t. standard deviation due to protective rare variants i.e., by 'MULTIPLIER * sigma'
-A/--meanshiftmax_rare_detrimental None maximum mean shift in quantitative value w.r.t standard deviation due to detrimental rare variants i.e., by 'MULTIPLIER * sigma', applicable to variable effects model
-B/--meanshiftmax_rare_protective None maximum mean shift in quantitative value w.r.t standard deviation due to protective rare variants i.e., by 'MULTIPLIER * sigma', applicable to variable effects model
-c/--meanshift_common_detrimental 0.0 mean shift in quantitative value w.r.t standard deviation due to detrimental common variants i.e., by 'MULTIPLIER * sigma'
-d/--meanshift_common_protective 0.0 mean shift in quantitative value w.r.t standard deviation due to protective common variants i.e., by 'MULTIPLIER * sigma'

BLNR & ELNR model options

Option Default Description
-a/--meanshift_rare_detrimental 0.0 mean shift in quantitative value w.r.t standard deviation due to detrimental rare variants i.e., by 'MULTIPLIER * sigma'
-b/--meanshift_rare_protective 0.0 mean shift in quantitative value w.r.t. standard deviation due to protective rare variants i.e., by 'MULTIPLIER * sigma'
-A/--meanshiftmax_rare_detrimental None maximum mean shift in quantitative value w.r.t standard deviation due to detrimental rare variants i.e., by 'MULTIPLIER * sigma', applicable to variable effects model
-B/--meanshiftmax_rare_protective None maximum mean shift in quantitative value w.r.t standard deviation due to protective rare variants i.e., by 'MULTIPLIER * sigma', applicable to variable effects model
-c/--meanshift_common_detrimental 0.0 mean shift in quantitative value w.r.t standard deviation due to detrimental common variants i.e., by 'MULTIPLIER * sigma'
-d/--meanshift_common_protective 0.0 mean shift in quantitative value w.r.t standard deviation due to protective common variants i.e., by 'MULTIPLIER * sigma'
--QT_thresholds [0.5, 0.5] lower/uppwer percentile cutoffs for quantitative traits in extreme QT sampling

show command option

Option Default Description
<args> None type of information to display, which can be 'tests' for a list of all association tests, 'test TST' for details of an association test TST, 'FILENAME.csv' for all column names in a csv file, 'FILENAME.csv [colnames]' for values of columns in a csv file; 'FILENAME.SEQPowerDB' for all table names in a SEQPower database file, 'FILENAME.SEQPowerDB TABLE' for all column names in a table, 'FILENAME.SEQPowerDB TABLE [colnames]' for values of specified columns in a table, and 'FILENAME.SEQPowerDB TABLE [colnames] --condition QUERY' for filtered/formatted values of columns in a table. Wildcard symbol '*' for colnames is allowed.
--border full table border

execute command option

Option Default Description
-s/--sliding None specify variable parameters
-f/--fixed None specify fixed parameters
--plot False generate plot instead of running simulations
--dry_run False print generated commands to screen instead of executing them