Population Parameters
FOUNDER_Effective_Size
- Description: Used to generate the population history of the haplotypes generated from MaCS. There are multiple default scenarios and represent a wide range of LD patterns, or one can specify a custom effective population size and population history. Each scenario has a slightly different population history parameter (i.e. “eN”). Lastly, the population history can be a single value with no historical population. A description is outlined HERE.
- Options:
- Ne70: A scenario that generates a large amount of short range LD.
- Ne100_Scen1: A scenario that generates moderate amount of short range LD.
- Ne100_Scen2: A scenario that generates moderate amount of short range LD.
- Ne250: A scenario that generates very little short range LD.
- Ne1000: A scenario that generates very little short range LD.
- CustomNe: Read in own population history parameters.
- Integer value(> 1): Utilizes the value as the effective population size and no population history assumed.
- Usage: 'FOUNDER_Effective_Size: Ne70'.
- Type: Mandatory.
MALE_FEMALE_FOUNDER
- Description: Sets the number of founder male and female individuals along with the method founders were selected and how many generations it occured.
- Options:
- Integer value: Number of male founders.
- Integer value: Number of female founders.
- random: At the current only random selection can be utilized.
- Integer value: Number of generations conducted.
- Usage: 'MALE_FEMALE_FOUNDER: 50 600 random 5'.
- Type: Mandatory.
VARIANCE_A
- Description: Variance due to additive gene action and/or correlation between additive QTL effects if two traits are simulated.
- Options:
- One Trait (double): additive genetic variation.
- Two Trait (double double double): additive genetic variance for trait 1, correlation between additive QTL effects for trait 1 and 2 and additive genetic variance for trait 2.
- Usage: 'VARIANCE_A: 0.25'.
- Type: Mandatory.
VARIANCE_D
- Description: Variance due to dominant gene action.
- Options:
- One Trait (double): dominance genetic variance.
- Two Trait (double double ): dominance genetic variance for trait 1 and trait 2.
- Usage: 'VARIANCE_D: 0.05'.
- Type: Optional. Default is 0.0.
- Note:
Care needs to be taken in choosing the additive and domi- nance variance and its implications on the number of QTL that display over-dominance or partial-dominance. Parameters to adjust include the QTL MAF frequency, mean and standard deviation of the normal distribution for dominance effects and the ratio of additive to dominance variance.
VARIANCE_R
- Description: Variance due to environmental effects (i.e. residual).
- Options:
- One Trait (double): environmental variance.
- Two Trait (double double double): environmental variance for trait 1, correlation between environmental effects for trait 1 and 2 and environmental variance for trait 2.
- Usage: 'VARIANCE_R: 0.75'.
- Type: Optional. Default is that total variance is equal to 1.0 and a null correlation between traits if applicable.