Managing datasets with PLINK
Here, we will manage our dataset using PLINK. We will create subsets of our main dataset (from the HapMap project) that are suitable for analysis in the following recipes.
Warning
Note that neither PLINK nor any similar programs were developed for their file formats. There was probably no objective to create a default file standard for population genetics data. In this field, you will need to be ready to convert from format to format (for this, Python is quite appropriate) because every application that you will use will probably have its own quirky requirements. The most important point to learn from this recipe is that it’s not formats that are being used, although these are relevant, but a ‘file conversion mentality’. Beyond this, some of the steps in this recipe also convey genuine analytical techniques that you may want to consider using, for example, subsampling or Linkage Disequilibrium- (LD-) pruning.
