SnpEff: Genetic variant annotation and effect prediction toolbox

SnpEff is a variant annotation and effect prediction tool. It
annotates and predicts the effects of variants on genes (such as amino
acid changes).

Input: The inputs are predicted variants (SNPs, insertions, deletions
and MNPs). The input file is usually obtained as a result of a
sequencing experiment, and it is usually in variant call format (VCF).

Output: SnpEff analyzes the input variants. It annotates the variants
and calculates the effects they produce on known genes (e.g. amino
acid changes).

This also installs SnpSift, a toolbox that allows you to filter and
manipulate annotated files. Once your genomic variants have been
annotated, you need to filter them out in order to find the
"interesting / relevant variants". Given the large data files, this is
not a trivial task (e.g. you cannot load all the variants into XLS
spreadsheet). SnpSift helps to perform this VCF file manipulation and
filtering required at this stage in data processing pipelines.

If you are using SnpEff or SnpSift, please cite:
A program for annotating and predicting the effects of single
nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang
le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin).
2012 Apr-Jun;6(2):80-92. PMID: 22728672