Admixture

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:

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

Execute commands in the code block below:

Run Admixture

#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)

Instructions for doing the exercise on TACC:

download PLINK

#download the exercise_files
 
wget http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20171102.zip
unzip plink2_linux_x86_64_20171102.zip

Download the appropriate version of PLINK into the exercise directory: