#### Script to run Admixture with Junierpus and Berberis ddRAD data
### Alicia Mastretta Yanes 2018

#### Admixture

## For Juniperus
mkdir -p ../genetic/JmINGP/out.noreplicates/popstructure
cd ../genetic/JmINGP/out.noreplicates/popstructure

# recode plink to needed formats
cp ../batch_1.plink.* ./
plink --file batch_1.plink --maf 0.05 --geno .2 --make-bed --out batch_1.plink --noweb --allow-no-sex

# run admixture using multithreaded mode, fixed random seed and corss-validation procedure to choose the correct value
for K in 1 2 3 4 5 6 7 8 9 10 11 12 13;
do ../../../../bin/admixture --cv batch_1.plink.bed  $K -j4  -s 21 | tee log${K}.out; done

# Check CV
grep -h CV log*.out

# back to bin
cd ../../../../bin

## For Berberis
mkdir -p ../genetic/BerSS/out.noreplicates/popstructure
cd ../genetic/BerSS/out.noreplicates/popstructure

# recode plink to needed formats
cp ../batch_1.plink.* ./
plink --file batch_1.plink --maf 0.05 --geno .2 --make-bed --out batch_1.plink --noweb --allow-no-sex

# run admixture using multithreaded mode, fixed random seed and corss-validation procedure to choose the correct value
for K in 1 2 3 4 5 6 7;
do ../../../../bin/admixture --cv batch_1.plink.bed  $K -j4  -s 21 | tee log${K}.out; done

# Check CV
grep -h CV log*.out