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Functional Annotation of VCF files

To annotate your vcf files, you need to run "new_run_snpeff.sh". You will need your vcf file, reference genome and snpeff.jar. SNPEFF is already an installed module by the HPCC Biocore. the reference genome is also a folder in snpeff. I am using GRCh38.v42 but you can switch to your desired genome

BEFORE RUNNING : Clone my repo and edit almost every line in new_run_snpeff.sh so that you specify your desired input, output folders, file locations, naming system and reference genome etc

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