TransVar - multiway annotator for precision medicine
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bin update to the way transvar configs; bug fix to ensembl input Jul 1, 2018
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README.md

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