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TransVar is a versatile annotator for 3-way conversion and annotation among genomic characterization(s) of mutations (e.g., chr3:g.178936091G>A) and transcript-dependent annotation(s) (e.g., PIK3CA:p.E545K or PIK3CA:c.1633G>A, or NM_006218.2:p.E545K, or NP_006266.2:p.G240Afs*50). It is particularly designed with the functionality of resolving ambiguous mutation annotations arising from differential transcript usage. TransVar keeps awareness of the underlying unknown transcript structure (exon boundary, reference amino acid/base) while performing reverse annotation (via fuzzy matching from protein level to cDNA level).

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TransVar features

• supports HGVS nomenclature
• supports input from gene name, transcript ID, protein ID, UniProt ID and other aliases.
• supports both left-alignment and right-alignment convention in reporting indels and duplications.
• supports annotation of a region based on a transcript-dependent characterization
• supports mutations at both coding region and intronic/UTR regions
• supports noncoding RNA annotation
• supports VCF inputs
• supports long haplotype decomposition
• supports single nucleotide variation (SNV), insertions and deletions (indels) and block substitutions
• supports transcript annotation from commonly-used databases such as Ensembl, NCBI RefSeq and GENCODE etc
• supports GRCh36, 37, 38 (human), GRCm38 (mouse), NCBIM37 (mouse)
• supports >60 other genomes available from Ensembl
• functionality of forward annotation.