Investigating population structure with Admixture

A typical analysis in population genetics was the one popularized by the program Structure (http://pritchardlab.stanford.edu/structure.html), which is used to study the population structure. This type of software is used to infer how many populations exist (or how many ancestral populations generate the current population) and how to identify potential migrants and admixed individuals. As Structure was developed quite some years ago when much less markers were genotyped (at that time, mostly a handful of microsatellites) and faster versions were developed, including one from the same laboratory called fastStructure (http://rajanil.github.io/fastStructure/). Here, we will use Python to interface with a program of the same type developed at UCLA called Admixture (https://www.genetics.ucla.edu/software/admixture/).

Getting ready

You will need to run the first recipe in order to use the hapmap10_auto_noofs_ld binary PLINK file. Again, we will use...