Investigating population structure with admixture

A typical analysis in population genetics was the one popularized by the program structure (https://web.stanford.edu/group/pritchardlab/structure.html), which is used to study population structure. This type of software is used to infer how many populations exist (or how many ancestral populations generated the current population), and to identify potential migrants and admixed individuals. The structure was developed quite some time ago, when far fewer markers were genotyped (at that time, this was 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 that was developed at UCLA, called admixture (https://dalexander.github.io/admixture/download.html).

Getting ready

You will need to run the first recipe in order to use the hapmap10_auto_noofs_ld...