Clinotator

Clinotator is a software tool to analyze ClinVar (a public archive of reports of the relationships among human variations and phenotypes) reports and extract essential parts of clinical reports. In the generation of a variations report, Clinotator uses a raw score comprising weighted pathogenicity, an average clinical assertion age, a predicted significance, and finally, ranking the impact based on the predicted significance. After inputting variants, Clinotator uses NCBI Entrez Programming Utilities (E-utilities) to query the ClinVar archive and generates variation reports with scoring metrics.

Topic

Genetic variation;Medical informatics;Data management

Detail

  • Operation: Annotation;Sequence database search;Variant classification

  • Software interface: Command-line user interface

  • Language: Python

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.4.0

  • Credit: Institutional funding from NorthShore University HealthSystem.

  • Input: vid,rsid,vcf

  • Output: -

  • Contact: Robert R. Butler III rbutler@northshore.org

  • Collection: -

  • Maturity: Stable

Publications

  • Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts.
  • Butler Iii RR, Gejman PV. Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts. F1000Res. 2018 Apr 13;7:462. doi: 10.12688/f1000research.14470.2. PMID: 29862020; PMCID: PMC5941247.
  • https://doi.org/10.12688/f1000research.14470.2
  • PMID: 29862020
  • PMC: PMC5941247.2

Download and documentation

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