A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.
Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile
A unified Python CLI for 30 bioinformatics file-format conversions (VCF, GFF3, GTF, BED, GenBank, FASTA, FASTQ, BAM, EIGENSTRAT, PLINK, MAF, MUMmer, HMMER, Newick) with consistent flags, batch mode, and a published Stage 1 benchmark vs convertf, plink2, AGAT, gffread, UCSC, EMBOSS, pyhmmer.
Python utilities for mapping 23andMe, AncestryDNA, FTDNA, and MyHeritage raw DNA files onto an EIGENSTRAT/PACKEDANCESTRYMAP panel, appending samples, exporting genotypes, and running PLINK missingness QC.
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