EGGS replicates missing genotype data in replicates, suggesting it can enhance genotype analysis across datasets.
Summary: We introduce Empirical Genotype Generalizer for Samples (EGGS) which accepts empirical genotypes with missing data and replicates the underlying dispersal and distribution of missing genotypes in other replicates. In addition, EGGS can remove phase, remove polarization, simulate deamination, create pseudohaploids, and convert between VCF, $ms$-style replicates, and EIGENSTRAT. Availability and Implementation: EGGS is written in the C programming language. Precompiled executables, source code, and the manual are available at https://github.com/TQ-Smith/EGGS
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Smith et al. (2025) studied this question.
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