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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#download#go to scratch cds #copy over the exercise_files 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 |
Download the appropriate version of PLINK into the exercise directory:
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