~~NOTOC~~

===== Table of Command Options =====
=== Common options ===
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^  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.  |
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=== LOGIT model options ===
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^  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  |
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=== PAR model options ===
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^  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  |
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=== LNR model options ===
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^  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'  |
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=== BLNR & ELNR model options ===
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^  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  |
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=== show command option ===
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^  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  |
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=== execute command option ===
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^  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  |
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