Tip

Note that neither PLINK nor any similar programs were developed because of their file formats. Probably, it had no objective to become 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 the ''file conversion mentality''. Apart from this, some of the steps in this recipe also convey genuine analysis techniques that you may want to consider using (for example, subsampling or Linkage Disequilibrium (LD) pruning).