bbglab/transvar repository overview

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).

https://github.com/zwdzwd/transvar⁠

How to run docker image:

docker run --rm -it bbglab/transvar:hg19 transvar panno -i 'PIK3CA:p.E545K' --ucsc --ccds