Converting EIGENSTRAT/PACKEDANCESTRYMAP to PACKEDPED
The files downloaded in the previous blog post are distributed as an EIGENSTRAT-style .geno/.snp/.ind dataset. This naming can be confusing: the .snp and .ind files are the usual EIGENSTRAT metadata files, but the .geno file may either be plain-text EIGENSTRAT or binary PACKEDANCESTRYMAP. 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. ...