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.
There isn't a windows version, so windows users should try it on TACC.
Instructions for doing the exercise on your personal computer:
Download and unzip the exercise files:
Download and unzip PLINK into the exercise directory:
https://www.cog-genomics.org/plink/2.0/
Download and unzip Admixture into the exercise directory:
https://www.genetics.ucla.edu/software/admixture/download.html
Navigate to the exercise directory and execute commands in the code block below:
Run Admixture with Mac
#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)
Instructions for doing the exercise on TACC:
Run Admixture on TACC
#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)
