https://popgenblog.com/tags/packedped/ Recent content in PACKEDPED on PopGen Blog Hugo -- 0.148.2 en-us Tue, 29 Jul 2025 15:30:00 +0000 https://popgenblog.com/posts/convert-eigenstrat-to-packedped/ Tue, 29 Jul 2025 15:30:00 +0000 https://popgenblog.com/posts/convert-eigenstrat-to-packedped/ <p>The files downloaded in the previous blog post are distributed as an EIGENSTRAT-style <code>.geno/.snp/.ind</code> dataset. This naming can be confusing: the <code>.snp</code> and <code>.ind</code> files are the usual EIGENSTRAT metadata files, but the <code>.geno</code> file may either be plain-text EIGENSTRAT or binary PACKEDANCESTRYMAP.</p> <p>PACKEDPED format allows for easier downstream processing using the <strong>PLINK</strong> toolset. With PLINK, it becomes straightforward to extract sample subsets, filter SNPs, and perform a wide range of analyses.</p>