RNA-seq data necessary to run the scripts are available on SRA under the BioProject ID PRJNA1128551.
trimPC/PW60.pl - performs trimming of the RNA-seq data
hisatPC/PW.pl - performs mapping of trimmed RNa-seq data to the genome reference
picard-markdup-index-PC/PW.pl - performs preparation of bamfiles for variant calling
haplotype-caller-PC/PW.pl - performs haplotype calling on individiual samples
gatk-genotypegvcfs.PC/PW.pl - performs joint genotyping on samples
Data tables necessary to run the scripts are available on figshare
eQTL_analysis_phenotype_data_incl.R - runs the SNP filtering and subsequent eQTL analysis