VAR-MD

VAR-MD has been designed to optimize annotation for Mendelian inherited disorders. It analyzes variants derived from whole genome or whole exome sequencing data coming from pedigrees. It outputs a list of putative pathogenic mutations based on inheritance models, genotype quality and allele frequency.

VARIANT

VARIANT (VARIant ANalysis Tool) is a web-based tool that interrogates several different databases in parallel. It utilizes dbSNP, 1000 Genomes, the GWAS catalog, OMIM and COSMIC.

VAT

VAT (Variant Analysis Tool) annotates variants which have been mapped on a transcript by the variant calling. It has been extensively used in the 1000 Genomes Project to annotate loss-of-function variants. Of note, together with ANNOVAR, VAT is the only annotation software that is capable of handling structural variations (e.g. large deletions/duplications).

VAAST

VAAST (Variant Annotation Analysis and Search Tool) uses an algorithm which is based on existing information on pathogenic variants to output a likelihood of pathogenicity. Differently from other software, it can also make predictions on non-coding variants.

SEATTLESEQ

SeattleSeq is a platform that integrates the output from other programs and databases to produce predictions on novel and known SNPs. It gives conservation scores, HapMap frequencies, Polyphen predictions and clinical associations. Its computations are also based on dbSNP via the Genome Variation Server.