Data tables necessary to run the scripts are available on figshare
trim.pl - performs trimming of the RNA-seq data
hisat.pl - performs mapping of trimmed RNa-seq data to the genome reference
picard-markdup-index.pl - performs preparation of bamfiles for variant calling
haplotype-caller.pl - performs haplotype calling on individiual samples
gatk-genotypegvcfs.pl - performs joint genotyping on samples
snp_genotyping_triads.R - associates genotype information with triads/homoeologs
association_genotype_expression.R - analyses the association between homoeolog expression and inherited genotype