GenoDiver

A Coalescent Forward in Time Simulation Toolkit

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  Similar to the previous examples, a bash script is outlined below that illustrates the impact of different genotyping strategies on the long term genetic trend when generating breeding values using single step genomic BLUP (ssgblup). The scenarios include no genotyping, only genotype a proportion or genotype every selection candidate. A total of 15 replicates were generated. After a scenario is done the directory where the replicates are saved 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 Example15.txt is still a file ##
rm -rf Example15.txt || TRUE
# Parameters that are the same #
echo '-| General |-' >> Example15.txt
echo 'SEED: 1500' >> Example15.txt
echo 'NREP: 15' >> Example15.txt
echo '−| Genome & Marker |−' >> Example15.txt
echo 'CHR: 5' >> Example15.txt
echo 'CHR_LENGTH: 87 87 87 87 87' >> Example15.txt
echo 'NUM_MARK: 1750 1750 1750 1750 1750' >> Example15.txt
echo 'QTL: 200 200 200 200 200' >> Example15.txt
echo '−| Population |−' >> Example15.txt
echo 'FOUNDER_Effective_Size: Ne250' >> Example15.txt
echo 'MALE_FEMALE_FOUNDER: 50 500 random 3' >> Example15.txt
echo 'VARIANCE_A: 0.35 0.15 0.35' >> Example15.txt
echo '−| Selection |−' >> Example15.txt
echo 'GENERATIONS: 15' >> Example15.txt
echo 'INDIVIDUALS: 50 0.4 500 0.2' >> Example15.txt
echo 'PROGENY: 1' >> Example15.txt
echo 'SELECTION: index_ebv high' >> Example15.txt
echo 'PHENOTYPE_STRATEGY1: 1.0 pheno_atselection 1.0 pheno_atselection' >> Example15.txt
echo 'PHENOTYPE_STRATEGY2: 1.0 pheno_afterselection 1.0 pheno_afterselection' >> Example15.txt
echo 'INTERIM_EBV: after_culling' >> Example15.txt
echo 'INDEX_PROPORTIONS: 0.20 0.80' >> Example15.txt
echo 'CULLING: index_ebv 12' >> Example15.txt
echo 'MATING: random' >> Example15.txt
echo '-| Output Options |-' >> Example15.txt
echo 'GENOTYPES: no' >> Example15.txt

## Used to loop across different phenotype proportions ##
prop=("0.20" "0.40" "0.60" "0.80")

##--------------------------------------------------------------------
## first do pblup
##--------------------------------------------------------------------
echo 'START: sequence' >> Example15.txt
echo 'EBV_METHOD: pblup' >> Example15.txt
## Run GenoDiver ##
./GenoDiver Example16.txt
## rename replicate output to reps_pblup_all ##
mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_pblup

##--------------------------------------------------------------------
## loop across different proportions based on ebv
##--------------------------------------------------------------------
for i in 0 1 2 3
do
     ## Remove parameters that are changing ##
     head -n 26 Example15.txt > Example15a.txt
     mv ./Example15a.txt ./Example15.txt
     ## echo in new paramters ##
     echo 'START: founder' >> Example15.txt
     echo 'EBV_METHOD: ssgblup' >> Example15.txt
     echo 'GENOTYPE_STRATEGY: 9' ${prop[i]} 'parents_ebv' ${prop[i]} 'parents_ebv' >> Example15.txt
     ## Run GenoDiver ##
     ./GenoDiver Example15.txt
     ## rename replicate output to reps_ebv_prop ##
     mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_ebv_${prop[i]}
done

##--------------------------------------------------------------------
## loop across different proportions based on random
##--------------------------------------------------------------------
for i in 0 1 2 3
do
     ## Remove parameters that are changing ##
     head -n 26 Example15.txt > Example15a.txt
     mv ./Example15a.txt ./Example15.txt
     ## echo in new paramters ##
     echo 'START: founder' >> Example15.txt
     echo 'EBV_METHOD: ssgblup' >> Example15.txt
     echo 'GENOTYPE_STRATEGY: 9' ${prop[i]} 'parents_random' ${prop[i]} 'parents_random' >> Example15.txt
     ## Run GenoDiver ##
     ./GenoDiver Example15.txt
     ## rename replicate output to reps_ebv_prop ##
     mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_random_${prop[i]}
done

##--------------------------------------------------------------------
## Genotype everyone
##--------------------------------------------------------------------
## Remove parameters that are changing ##
head -n 26 Example15.txt > Example15a.txt
mv ./Example15a.txt ./Example15.txt
## echo in new paramters ##
echo 'START: sequence' >> Example15.txt
echo 'GENOTYPE_STRATEGY: 9 1.0 parents_offspring 1.0 parents_offspring' >> Example15.txt
echo 'EBV_METHOD: ssgblup' >> Example15.txt
## Run GenoDiver ##
./GenoDiver Example15.txt
## rename replicate output to reps_all ##
mv ./GenoDiverFiles/replicates ./GenoDiverFiles/reps_all