GenoDiver

A Coalescent Forward in Time Simulation Toolkit

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  A bash script is outlined below that illustrates how to loop through different simulation scenarios. The following script may take a couple of hours to finish depending on the computing environment. The difference between the scenarios is how estimated breeding values (EBV) are estimated across individuals. The four methods to predict EBV are: a pedigree-based best linear unbiased prediction (BLUP) animal model, a genomic-based BLUP animal model, a run-of-homozygosity-based BLUP animal model and a Bayesian spike and slab marker effects model (BayesC). All three scenarios utilize the same founder sequence, which is generated by first using the 'sequence' option for the "START" parameter and then the remaining scenarios use the 'founder' option for the "START" parameter. In order to generate multiple replicates within each scenario, the "NREP" parameter is utilized and 15 replicates were generated within each scenario. The replicates are saved within the "GenoDiverFiles" directory for each scenario. If the directory isn't renamed, the next scenario will replace the files. Therefore, after a scenario is done the directory is renamed within the bash script.

##--------------------------------------------------------------------
## First generate parameter file. Put parameters to change at the very
## bottom of the file. That way you can use the 'head' linux command
## for the parameters that change and use the 'echo' linux command to
## add any new parameters.
##--------------------------------------------------------------------
## In case 4_Example.txt is still a file ##
rm -rf Example12.txt || TRUE

# Parameters that are the same #
echo '-| General |-' >> Example12.txt
echo 'SEED: 1500' >> Example12.txt
echo 'NREP: 15' >> Example12.txt
echo '−| Genome & Marker |−' >> Example12.txt
echo 'CHR: 3' >> Example12.txt
echo 'CHR_LENGTH: 150 150 150' >> Example12.txt
echo 'NUM_MARK: 4000 4000 4000' >> Example12.txt
echo 'QTL: 200 200 200' >> Example12.txt
echo '−| Population |−' >> Example12.txt
echo 'FOUNDER_Effective_Size: Ne100_Scen1' >> Example12.txt
echo 'MALE_FEMALE_FOUNDER: 50 400 random 5' >> Example12.txt
echo 'VARIANCE_A: 0.35' >> Example12.txt
echo '−| Selection |−' >> Example12.txt
echo 'GENERATIONS: 10' >> Example12.txt
echo 'INDIVIDUALS: 50 0.2 400 0.2' >> Example12.txt
echo 'PROGENY: 1' >> Example12.txt
echo 'SELECTION: ebv high' >> Example12.txt
echo 'CULLING: ebv 8' >> Example12.txt
echo 'MATING: random125 simu_anneal' >> Example12.txt

##--------------------------------------------------------------------
## First do PBLUP based EBV prediction
##--------------------------------------------------------------------
echo 'START: sequence' >> Example12.txt
echo 'EBV_METHOD: pblup' >> Example12.txt
## Run GenoDiver ##
./GenoDiver Example12.txt
## rename replicate output to rep_pblup ##
mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_pblup

##--------------------------------------------------------------------
## Then do GBLUP based EBV prediction
##--------------------------------------------------------------------
## Remove parameters that are changing ##
head -n 19 Example12.txt > Example12a.txt
mv ./Example12a.txt ./Example12.txt
## echo in new paramters ##
echo 'START: founder' >> Example12.txt
echo 'EBV_METHOD: gblup' >> Example12.txt
## Run GenoDiver ##
./GenoDiver Example12.txt
## rename replicate output to rep_gblup ##
mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_gblup

##--------------------------------------------------------------------
## Then do ROHBLUP based EBV prediction
##--------------------------------------------------------------------
## Remove parameters that are changing ##
head -n 19 Example12.txt > Example12a.txt
mv ./Example12a.txt ./Example12.txt
## echo in new paramters ##
echo 'START: founder' >> Example12.txt
echo 'EBV_METHOD: rohblup' >> Example12.txt
## Run GenoDiver ##
./GenoDiver Example12.txt
## rename replicate output to rep_rohblup ##
mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_rohblup

##--------------------------------------------------------------------
## Then do BAYESC based EBV prediction
##--------------------------------------------------------------------
## Remove parameters that are changing ##
head -n 19 Example12.txt > Example12a.txt
mv ./Example12a.txt ./Example12.txt
## echo in new parameters
echo 'START: founder' >> Example12.txt
echo 'EBV_METHOD: bayes' >> Example12.txt
echo 'BAYESOPTIONS: BayesC 10000 2000 6000 1000 5 fix 0.10' >> Example12.txt
## Run GenoDiver ##
./GenoDiver Example12.txt
## rename replicate output to rep_bayesC ##
mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_bayesC