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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
EGGS: Empirical Genotype Generalizer for Samples
T Quinn Smith1, Amatur Rahman1, Zachary A Szpiech1
1Department of Biology, The Pennsylvania State University, University Park, PA 16802.
None:
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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