EGGS: Empirical Genotype Generalizer for Samples

We introduce Empirical Genotype Generalizer for Samples (EGGS) which accepts empirical genotypes with missing data and replicates the distribution of missing genotypes along the empirical segment in other replicates. The empirical segment must have a number of sites less than the replicate. In addition, EGGS can remove phase, remove polarization, simulate deamination, simulate sequencing error, create pseudohaploids, and convert between Variant Call Format (VCF), ms-style replicates, and EIGENSTRAT/ANCESTRYMAP. When producing VCF files, EGGS is not limited to biallelic sites and assumes all samples are diploid.

EGGS is written in the C programming language. Precompiled executables, source code, the manual, and the analysis conducted in the paper are available at https://github.com/TQ-Smith/EGGS.