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heterPlotter package can plot heterozygosity information of hapmap(female and F1) files and pvalue information you use the same hapmap file to calculate GWAS, besides it can also draw the relative gene feature on the top of the plot
Archived code for analyses in "Genomic signatures of divergent ecological strategies in a recent radiation of Neotropical wild cats" (Ramirez et al. 2022, MBE)