PACKEDPED

The files downloaded in the previous blog post are in EIGENSTRAT format. In this post, we’ll look at how to convert them to PACKEDPED format. PACKEDPED format allows for easier downstream processing using the PLINK toolset. With PLINK, it becomes straightforward to extract sample subsets, filter SNPs, and perform a wide range of analyses. Downloading PLINK I use PLINK 1.9. While there is a newer version (2.0), I prefer 1.9 because it includes several features that were deprecated or removed in the newer release. ...