## script to set up and run snpEff

# Before running, open snpEff.config using emacs and add ITAG3.2 lines to snpEff.config:
## ITAG3.2 Solanum lycopersicum
#ITAG3.2.genome : ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa


cd /home/bioinfo/Programs/snpEff/

wget https://sourceforge.net/projects/snpeff/files/databases/v4_3/snpEff_v4_3_ITAG3.2.zip

unzip snpEff_v4_3_ITAG3.2.zip


cd /home/bioinfo/Desktop/Slch04_demo/variants/

java -jar /home/bioinfo/Programs/snpEff/snpEff.jar eff ITAG3.2 gatk_var.vcf > gatk_var_snpEff.out
