TransVar
| Overview | |
|---|---|
| Description | TransVar is a multi-way annotator for genetic elements and genetic variations. |
| Development Information | |
| GitHub | zwdzwd/transvar (opens in new tab) |
| URL | https://bioinformatics.mdanderson.org/transvar/ (opens in new tab) |
| Language | Python |
| Current version | 2.4.0 |
| License | The MIT License (opens in new tab) |
| 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 (opens in new tab) |
| Help and Support | |
| Contact | Ken Chen |
| Discussion | Issues On GitHub (opens in new tab) |
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 (opens in new tab) and online user's guide (opens in new tab).