Admixture is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets (publication; website).
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#(On TACC) #navigate to directory cd intro_to_rad_2018/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 file corals.3.Q to your computer and use plot_admixture.R to plot the results #Contrast the results with PCA plotted from the same data (PCA exercise) |
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