Using Admixture

The following script requires a few pieces…broken down below:

Programs

  • angsd installed
  • NGSadmix in your ~/bin (comes as part of NGStools, but may need to copy exec into bin)

Folders

  • I use a out_slurms folder to catch the slurm output
  • The script can/will create results_admix folder
  • assumes my bamlist lives in a bamlists folder

Files

  • a bamlist of with all samples you are interested in assessing admixture


The Output (.opt file)

You should end up with a file that ends in admixX.qopt, where X is the k-groups you chose. This file can be plotted a number of ways.

  • Use Rscripts to plot (see:)
  • Try the online pophelper to make admixture graphs