Introduction

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.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).Supplementary data are available at Bioinformatics online.

Publications

  1. A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.
    Cite this
    Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA, 2015-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Reece K Hart
    Developer

    Invitae Inc., San Francisco, United States of America

  2. Rudolph Rico
    Developer

    Invitae Inc., San Francisco, United States of America

  3. Emily Hare
    Developer

    Invitae Inc., San Francisco, United States of America

  4. John Garcia
    Developer

    Invitae Inc., San Francisco, United States of America

  5. Jody Westbrook
    Developer

    Invitae Inc., San Francisco, United States of America

  6. Vincent A Fusaro
    Investigator

    Invitae Inc., San Francisco, United States of America

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Summary
AccessionBT006368
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByVincent A Fusaro