# Phenotypic mean =    0.000 (SD=   1.000)

# QTL allele prop =     0.500
# QTL genot means =    -1.000    0.000    1.000

# VQ              =    0.500 (  50.0%)
# VA              =    0.000 (   0.0%)
# VC              =    0.000 (   0.0%)
# VE              =    0.500 (  50.0%)


set locus mztwin    qua          
set locus trait     qua          
set loc   marker001 marker 0.00  
set loc   marker002 marker 10.00 
set locus qtl       marker 15.00 
set loc   marker003 marker 20.00 
set loc   marker004 marker 30.00 
read pedigree gbye.ped                                                                        
set ple -1
run
set loc env qua
env=2*rand+1
set loc qfac qua
factor qtl qfac
if (qfac==1) then trait=-1 + env*rnorm
if (qfac==2) then trait=env*rnorm
if (qfac==4) then trait=1 + env*rnorm

write sim1.ped
write loc sib sim1.in sim1.ped
$ sp2R sim1.in > sim1.rta