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VariantTools: an extensible framework for developing and testing variant callers.

Michael Lawrence1, Robert Gentleman2

  • 1Department of Bioinformatics, Genentech, South San Francisco, CA, USA.

Bioinformatics (Oxford, England)
|October 14, 2017
PubMed
Summary
This summary is machine-generated.

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VariantTools is a new framework for developing and testing variant callers. This flexible, modular system aids in reproducibly tallying, filtering, flagging, and annotating genetic variants for various applications.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Variant calling is crucial for distinguishing true genetic polymorphisms from sequencing errors.
  • The optimal variant calling strategy depends on sample characteristics, sequencing methods, and research objectives.

Purpose of the Study:

  • To introduce VariantTools, an extensible framework for the development and evaluation of variant calling software.
  • To provide tools for reproducible variant data management, including tallying, filtering, flagging, and annotation.

Main Methods:

  • VariantTools is designed as an extensible, modular, and flexible framework.
  • The system facilitates reproducible variant analysis workflows.
  • It is designed to interoperate with existing bioinformatics analysis software.

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Main Results:

  • VariantTools offers comprehensive facilities for managing genetic variants.
  • The framework supports reproducible tallying, filtering, flagging, and annotation of variants.
  • Its modular design allows tuning for specific use cases and integration into established workflows.

Conclusions:

  • VariantTools provides a flexible and robust platform for variant caller development and testing.
  • The framework enhances the reproducibility and efficiency of genetic variant analysis.
  • VariantTools is readily embeddable into existing bioinformatics pipelines.