Genometric Analysis Simulation Program (GASP)

Parameter Descriptions

title

Any text up to 55 characters; may be used to identify the run

#_of_reps

Number of separate samples to be generated

unrelated

Unrelated individuals generated

sibship

Sibships generated

nuclear

Nuclear families generated

ceph

CEPH families generated (sibship plus parents and grandparents)

simple

Simple pedigrees generated

#_of_families

Number of families in each sample (1-5000)

fam_size

Maximum family size, including parents (>= 1)

fixed

Fixed sibship size

random

Randomly generated sibship size

sib_size

Size of sibship (>= 0), if fixed
(if family type is unrelated, must be 0;
if family type is nuclear or sibship, must be fam_size - 2;
if family type is ceph, must be fam_size - 6)

nb_par1

Negative binomial parameter 1 (1-15), if sibship size is random

nb_par2

Negative binomial parameter 2 (>0, <1), if sibship size is random

int_seed

Seed for random number generator (9-digit integer)

locus_name

Name for a single-locus component

n_alleles

Number of alleles for a particular single-locus component

recomb_frac

Recombination fraction between a particular single locus and the previously specified one

al_i_name

Name of i'th allele of a particular single locus component (1 character)

al_i_freq

Relative frequency of i'th allele of a particular single locus component (these must sum to 1 for a particular single locus component)

gt_ij_val

Genotypic value for a genotype formed by i'th and j'th alleles, for a particular single locus component

gt_ij_var

"Genotypic variance" for a genotype formed by i'th and j'th alleles, for a particular single locus component
(0 for a locus with a "qualitative" effect, such as a marker locus, or 1 for a locus with a "quantitative" effect)

env_name

Name of a trait-specific environment component

polygn_name

Name of a polygenic component

covar_name

Name of a covariate component

com_env_name

Name of a common sibship environment component

trt_name

Name of a trait

n_trt_cmpts

Number of components involved in a particular trait

trt_cmpti

Name of i'th component of a particular trait (one of the component names already defined)

trt_cmpti_%var

Proportion of the phenotypic variance of a particular trait due to its i'th component