Cacao marker harmonization and revision diagnostics

Analysis software for Coordinate conventions and marker density shape coverage of cacao aroma loci. The marker harmonization pipeline (3.0.0) analyzes marker identity, reference-derived SNP coordinates, positional coverage, matched gene backgrounds and conditional unphased genotype-dosage correlations. Revision diagnostics (1.0.0) evaluate filter-specific recovery, identifier links, coordinate conventions, adjusted genotype correlations, peak-level coordinate anchors and sensitivity to gene-background matching. The harmonization pipeline starts from provider workbooks and the Criollo v2 reference. The diagnostics use Supplementary Data S1 and the provider workbooks. Instructions specify the inputs, analysis settings and validation checks. Source workbooks and reference files are obtained from their providers.