Admixture

#move the admixture executable into the exercise directory
mv admixture_macosx-1.3.0/admixture .
 
#convert the VCF file into .ped file for input into Admixture
./plink2 --vcf corals.vcf --make-bed --out corals --allow-extra-chr
 
#Run Admixture on the .ped file made by PLINK specifying an expectation of three ancestral populations
./admixture corals.bed 3
 
#Plot the results using plot_admixture.R

#Contrast the results with PCA plotted from the same data (PCA exercise)

#go to scratch
cds
 
#copy over the exercise file
cp /work/02260/grovesd/lonestar/intro_to_rad_2017/admixture_exercise.zip .
 
#unzip it and go to the directory
unzip admixture_exercise.zip
cd admixture_exercise

#download and unzip PLINK
wget http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20171102.zip
unzip plink2_linux_x86_64_20171102.zip
 
#download and unzip Admixture
wget https://www.genetics.ucla.edu/software/admixture/binaries/admixture_linux-1.3.0.tar.gz --no-check-certificate
tar -zxvf admixture_linux-1.3.0.tar.gz
 
#move the admixture executable to the exercise directory
mv admixture_linux-1.3.0/admixture .
 
#convert the VCF file into .ped file for input into Admixture
./plink2 --vcf corals.vcf --make-bed --out corals --allow-extra-chr
 
#Run Admixture on the .ped file made by PLINK specifying an expectation of three ancestral populations
./admixture corals.bed 3
 
#move the files corals.3.Q, plot_admixture.R, and names.txt to your computer and use plot_admixture.R to plot the results
#Contrast the results with PCA plotted from the same data (PCA exercise)