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VariMAT – Variation and Mutation Annotation Toolkit

VariMAT is a web-based toolkit for comprehensive annotation of human single nucleotide variations (SNVs) and shot insertions/deletions (indels). VariMAT utilizes different databases and public resources including UCSC, GENCODE, ENCODE, Ensembl, dbSNP, NCBI, HapMap, and the 1000-genomes project. The various annotation types implemented in the toolkit are: genomic, functional, common variation and disease annotation. Genomic annotation includes genes, splice-sites, UTRs, repeats, conserved transcription factor binding sites (TFBS), regulatory regions (from ChiP-seq), conserved enhancers, CpG-Islands, miRNAs and promoter regions. The functional annotations implemented into the toolkit are variant class prediction (silent, missense, nonsense, inframe and framshift), polyPhen and gene ontology summary. Various disease annotation includes are OncoMD, GWAS, ClinVar, SNPedia. In addition, the tool also compares the variant with several published personal genomes and common variation databases – dbSNP, 1000-genomes, HapMap. It accepts input in variant call format (vcf) and 23andMe format. VariMAT is capable of annotating several thousand variants in minutes. The complete annotation result can be easily exported to the local desktop computer. It also generates several tables and plots that can be used for publications.

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