Nearly 100 years ago, Sewall Wright developed F-statistics to quantify inbreeding effects at a certain level of population subdivision. FST is the most widely used of these statistics and is mostly interpreted as the genetic variation caused by the population structure.
You will need to have run the first two recipes and should have the hapmap10_auto_noofs_2.gp and hapmap10_auto_noofs_2.pops files. We will also use the metadata file downloaded in the first recipe. For the type of comparison that we will perform here, it's important to assure that there is little relatedness among sampled individuals, so we want to remove the offspring at the very least. For efficiency, we will use only chromosome 2 subsampled at 10 percent.
For this code to work, you will need to install Genepop from http://kimura.univ-montp2.fr/~rousset/Genepop.htm. We will use the interface provided by Biopython to execute Genepop and parse its output files. These requirements are the...