SNP Allocation For Estimating Heritability (SAFE-<i>h</i>²): A tool to explore genomic origins of phenotypes for estimation of SNP heritability using additive-only allelic effects or additive and non-additive allelic effects

SAFE-h2 is developed under an academic research study to provide proper estimates of SNP heritability. For this, SAFE-h2 creates heritability profiles to prevent SNPs with illogical negative contributions to heritability. It also minimizes the contributions by false-positive SNP hits. Finally, SAFE-h2 can perform a joint analysis on both additive and non-additive allelic effects. Therefore, it also provides the chance for GWASs to perform linear association tests while capturing both additive and non-additive effects. Software Availability: SAFE-h2 (SNP Allocation For Estimating Heritability) contains the compiled SAFE-h2 scripts with related installation and usage manual (Download link: https://github.com/SAFE-h2/SAFE-h2-v2024-1). An old version also exists at https://github.com/SAFE-h2/SAFE-h2. Read the related research article “On the Genetic Origins of Phenotypes in Genome-Wide Association Studies: The SNP Allocation For Estimating Heritability (SAFE-h2) Tool to Explore Additive-only Allelic Effects or Additive and Non-Additive Allelic Effects” (doi: https://doi.org/10.1101/2023.08.28.555092; https://www.biorxiv.org/content/10.1101/2023.08.28.555092v6) for the full study and descriptions. Citation: Behrooz Darbani, Mogens Nicolaisen. On the Genetic Origins of Phenotypes in Genome-Wide Association Studies: The SNP Allocation For Estimating Heritability (SAFE-h2) Tool to Explore Additive-only Allelic Effects or Additive and Non-Additive Allelic Effects. doi: https://doi.org/10.1101/2023.08.28.555092 Contact: [e-mail], [e-mail]