snpEff is a small, fast, reliable variant effect predictor (SNP, MNP and InDels) for genomic data.
snpEff is integrated with Galaxy so it can be used either as a command line or as a web application.
A variant can be either a SNP (single-nucleotide polymorphism), an InDel (insertion or deletion) or a MNP (multiple-nucleotide polymorphism).
Here are some key features of "snpEff":
· Makes over a millon predictions per minute.
· You can add custom genomes and annotations
· Integrated with Galaxy
· Integrated with GATK
· Supports multiple codon table (e.g. mithoncondrial DNA)
· Java 1.6 or later
What's New in This Release: [ read full changelog ]
· Over 8,500 genomes supported.
· All ENSEMBL (version 18) : Bacteria, Fungi, Metazoa, Plants and Protist genomes added.
· NextProt annotaions added
· Motif annotations support added
· SnpSift: GeneSet annotations
· SnpEff count: Genomic region statistics counting reads, variants, intervals, etc.