TransVar

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TransVar

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Overview
Description	TransVar is a multi-way annotator for genetic elements and genetic variations.
Development Information
GitHub	zwdzwd/transvar
URL	https://bioinformatics.mdanderson.org/transvar/
Language	Python
Current version	2.4.0
License	The MIT License
Status	Active
Last updated	September 7, 2018
References
Citation	Zhou, W., Chen, T., Chong, Z., et al., TransVar: a multilevel variant annotator for precision genomics, Nature Methods 12 p1002 (2015). https://doi.org/10.1038/nmeth.3622
Help and Support
Contact	Ken Chen
Discussion	Issues On GitHub

TransVar

TransVar is a multi-way annotator for genetic elements and genetic variations.

It operates on genomic coordinates (e.g., chr3:g.178936091G>A) and transcript-dependent cDNA as well as protein coordinates (e.g., PIK3CA:p.E545K or PIK3CA:c.1633G>A, or NM_006218.2:p.E545K, or NP_006266.2:p.G240Afs*50), and was designed to resolve ambiguous mutation annotations arising from differential transcript usage.

TransVar supports

HGVS nomenclature
both left-alignment and right-alignment convention in reporting indels.
annotation of a region based on a transcript dependent characterization
single nucleotide variation (SNV), insertions and deletions (indels) and block substitutions
mutations at both coding region and intronic/UTR regions
transcript annotation from commonly-used databases such as Ensembl, NCBI RefSeq and GENCODE etc
UniProt protein id as transcript id
GRCh36, 37, 38
forward annotation.

Please visit the web interface web interface and online user's guide .

Department of Bioinformatics and Computational Biology

TransVar