Variant annotation with SnpEff for human tumor samples

DNA sequencing often aims to reveal special genetic features or differences between sample and reference genome. These genetic variants are commonly stored in VCF-files, where every line describes one feature - its position on chromosome, nucleotides of reference and sample sequence, quality, sequencing depth and so on. But the aim of the experiment is generally not just limited to obtain such set of variants but also to interpret them. We need to find which among the discovered variants fall into genes and which to intergenic spaces.