Bioinformatics with Python Cookbook

Computing F-statistics

Nearly 100 years ago, Sewall Wright developed F-statistics to quantify inbreeding effects at a certain level of population subdivision. F_ST is the most widely used of these statistics and is mostly interpreted as the genetic variation caused by the population structure.

Getting ready

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 ...