Original title: Unified Multi-caller Ensemble (UME) generates an unbiased maize haplotype map for variable coverage whole genome data
Authors: Miguel Vallebueno-Estrada,Kelly Swarts
In this article, the authors present a new haplotype map called HapMap. This map characterizes over 64.5 million single nucleotide polymorphisms (SNPs) in maize (Zea mays) across 818 individuals from diverse backgrounds. The purpose of this HapMap is to balance the variation obtained from different sources in order to minimize biases in diversity studies. The individuals included in this study come from various experimental setups and coverages, which creates challenges for standard SNP callers. To overcome this, the authors introduce a new approach called Unified Multi-Caller Ensemble (UME), which enhances variant calling accuracy in low-coverage and mixed-coverage datasets. UME corrects for coverage bias and outperforms individual strategies, leading to unbiased variant discovery and genotype calling. This HapMap database provides a comprehensive representation of maize accessions and offers crucial context for interpreting diversity, particularly for natural diversity and paleogenomic analyses.
Original article: https://www.biorxiv.org/content/10.1101/2023.12.07.570552v1