TransVar - multiway annotator for precision medicine
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.
bin update to the way transvar configs; bug fix to ensembl input Jul 1, 2018

TransVar Travis-CI Build Status License

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). 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).

User Guide is here.

Try out transvar via pip

sudo pip install transvar

or locally

pip install --user transvar

To upgrade from previous installation, you can

pip install -U transvar

This is a continued TransVar implementation from what was hosted at