Changes

default is '''OFF''', but will be automatically turned on for families larger than 25 individuals.

default is '''OFF''', but will be automatically turned on for families larger than 25 individuals.

===--traitIncreasing===

===--traitIncreasing [ON|OFF]===

[ON|OFF]: default is '''OFF'''; can be used together with '''--traitDecreasing''' options or used alone.

default is '''OFF'''; can be used together with '''--traitDecreasing''' options or used alone.

===--traitDecreasing===

===--traitDecreasing [ON|OFF]===

[ON|OFF]: default is '''OFF'''; can be used together with '''--traitIncreasing''' options or used alone.

default is '''OFF'''; can be used together with '''--traitIncreasing''' options or used alone.

==Trait==

==Trait==

===--inverseNormal===

===--inverseNormal [ON|OFF]===

[ON|OFF]: default is '''OFF'''; '''ON''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option).  

default is '''OFF'''; '''ON''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option).  

===--useCovariates===

===--useCovariates [ON|OFF]===

[ON|OFF]: default is '''OFF'''; '''ON''' will adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file).  

default is '''OFF'''; '''ON''' will adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file).  

===--traitName===

===--traitName [string]===

[your.trait.name.in.string]: default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).

default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).

==Parameters==

==Parameters==

===--maf===

===--maf [double]===

[your.preferred.frequency.value]:default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.

default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.

===--effect===

===--effect [double]===

[your.preferred.effect.size]:default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.

default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.

==MCMC==

==MCMC==

===--seed===

===--seed [double]===

===--chains===

===--chains [int]===

===--iterations===

===--iterations [int]===