Aligned SNP Data for CDBN Genomics in Hapmap and Numeric Format

This dataset contains SNP data for replication of the genome-wide association results in the paper “Genetic Associations in Four Decades of Multi-Environment Trials Reveal Agronomic Trait Evolution in Common Bean”. It contains SNP data for 348 genotypes of common bean (Phaseolus vulgaris), grown as part of the Cooperative Dry Bean Nursery. It contains this data in both hapmap and numeric format. To create the hapmap data, aligned SNP data was created from raw sequence data using the pipeline at https://github.com/Alice-MacQueen/SNP-calling-pipeline-GBS-ApeKI . It was then imputed using FILLIN and filtered to contain only SNPs with a minor allele frequency of 5% or higher, and with missing data of 120 individuals or fewer. The hapmap file was used to create single chromosome files in numerical format, which GAPIT accepts, using GAPIT.