title: A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.
abstract: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics.
  
  
  METHODS
  The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs).
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Invitae Inc., San Francisco, CA 94107 and 23andMe Inc., Mountain View, CA 94043, USA Invitae Inc., San Francisco, CA 94107 and 23andMe Inc., Mountain View, CA 94043, USA.
authors.forename: Reece K
authors.initials: RK
authors.lastname: Hart
authors.affiliation: Invitae Inc., San Francisco, CA 94107 and 23andMe Inc., Mountain View, CA 94043, USA.
authors.forename: Rudolph
authors.initials: R
authors.lastname: Rico
authors.affiliation: Invitae Inc., San Francisco, CA 94107 and 23andMe Inc., Mountain View, CA 94043, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Hare
authors.affiliation: Invitae Inc., San Francisco, CA 94107 and 23andMe Inc., Mountain View, CA 94043, USA.
authors.forename: John
authors.initials: J
authors.lastname: Garcia
authors.affiliation: Invitae Inc., San Francisco, CA 94107 and 23andMe Inc., Mountain View, CA 94043, USA.
authors.forename: Jody
authors.initials: J
authors.lastname: Westbrook
authors.affiliation: Invitae Inc., San Francisco, CA 94107 and 23andMe Inc., Mountain View, CA 94043, USA.
authors.forename: Vincent A
authors.initials: VA
authors.lastname: Fusaro
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D014644:Genetic Variation / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation; D012984:Software; D009626:Terminology as Topic