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
#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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