Scripts to run simulations.

The runSimulator_glost.sh script is used to set all the parameters for the analysis. These parameters are:
#### Switches
# Genome simulation switch (0=off, 1=on)
simu_geno=0
# Permutation switch (0=off, 1=on)
permut=1

############################################################################################################
#### Parameters
nbrun=1000
# Nb individuals, used only if simu_geno=1
nb_ind=1000                                    
# Min MAF threshold (for pheno simulation)        
minmaf=0.05
# Max MAF threshold (for pheno simulation)
maxmaf=0.5
# Trait heritability (for pheno simulation)                                            
her=0.8
# Nb of causal SNPs
nb_snps=10
# Nb of phenotype replicates
replicates=1
# Nb permutations, used only if permut=1                                    
nb_permut=100

This script will call run_FaSTLMM.py which will then run the associations, the permutations according to the defined parameters.

Note: this script only writes the command to be executed in a text file, as the commands were executed on a supercomputer with specific rules for parallel computing.