SAP_WGS

Whole-genome sequencing of the Sorghum Asssociation Panel

Analysis scripts:

circos - Circos configuration and execution scripts
Fst - scripts for Fst calculations
genomic_prediction - genomic selection scripts
gwas - scripts for GEMMA
hecaton - scripts for copy number variant calling
impute_filter - Beagle and BCFtools scripts
metrics - LD, nucleotide diversity, PCA
misc_scripts - snpEff, extract gene features from SNPs
variant_calling - scripts for GATK variant calling pipeline
Gene features were extracted using https://github.com/jlboat/features_from_snps
QTL were isolated from the Sorghum QTL Atlas using https://github.com/jlboat/query_qtl_atlas