CP-NAM

Scripts used to process the Sorghum Carbon-Partitioning NAM

Basic analysis steps:

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

QTL - per 11 populations

GWAS - scripts each model

misc - epistasis, snpEff, extract gene features from SNPs, fix VCF reference alleles

plots - scripts used to generate manuscript figures