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
). 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
Pre-built docker images can be found here
This is a continued TransVar implementation from what was hosted at https://bitbucket.org/wanding/transvar.