We will go through a simple and more complex example on how to use PCAngsd with visualization of the data.

PCA with admixture aware priors

This example will perform a PCA analysis on 1000 genotype likelihoods.

First, set the paths to the program and the input file every time you open a new terminal window.

Set the path to PCAngsd, for example:

NGSADMIX=~/Software/NGSadmix

Test the link

ls $NGSADMIX

Set the path to the input file, for example:

PCAngsdTutorial