in Java. It takes as input a VCF file of variants and a data base of genomic features
and outputs a VCF file that has an <code>ANNO</code> field within the VCF’s <code>INFO</code> column that
provides information about what genes (if any) the variant resides within, and what
effect the variation at that site might have on the expression of the gene.</p>
<p>The standard way to run SnpEff is to simply name the reference genome for the species
you are using, and then have SnpEff download the appropriate data