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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).

Environment Modules

Run module spider transvar to find out what environment modules are available for this application.

System Variables

  • HPC_TRANSVAR_DIR - installation directory
  • HPC_TRANSVAR_BIN - executable directory