Admixture is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets (publication; website).
Exercise:
This exercise is to be done on your personal computer or on TACC.
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https://www.genetics.ucla.edu/software/admixture/download.html
Execute Navigate to the exercise directory and execute commands in the code block below:
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| #go to exercise directory
cd admixture_exercise
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#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) |
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Instructions for doing the exercise on TACC:
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#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
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Download the appropriate version of PLINK into the exercise directory:
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#Contrast the results with PCA plotted from the same data (PCA exercise) |