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.,
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
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 https://bitbucket.org/wanding/transvar.