VAT - annotation on genomic variants with function and frequency

The Variant Annotation Tool (VAT) consists of a set of modules to annotate genetic variants including single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and structural variants (SVs). This software package also contains a program to aggregate these variants at the gene level. Subsequently, an image is generated for each gene to visualize the functional impact of the annotated variants. This information can then be viewed and shared using a web-interface. In addition to annotation of the coding variants, this tool also integrates allele frequencies and genotype data providing population-specific information from published high quality variation databases such as 1000 Genomes Project

working on VCF file format.

http://info.gersteinlab.org/VAT