Scripts used to process the Sorghum Carbon-Partitioning NAM
data - pericarp and testa phenotypes in CSV format
tassel - scripts used to generate variant calls
imputation and filtering - Beagle and VCFtools scripts
basic metrics - LD, nucleotide diversity, PCA
GWAS - scripts each model
misc - epistasis, snpEff, extract gene features from SNPs, fix VCF reference alleles
plots - scripts used to generate manuscript figures