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Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms

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Variant Calling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2493))

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Abstract

Next-generation sequencing technologies have been widely used to query genetic variants in normal individuals as well as in those with diseases. Large-scale structural variations are a common source of genetic diversity in human population, and some of them have significant contributions to the etiology of diseases. However, the detection of large-scale structural variations from sequencing data remains challenging. Here, we describe Meerkat—an algorithm which can reliably detect structural variations from Illumina short-read sequencing data at basepair resolution. A unique feature of Meerkat is that it can infer the variant forming mechanisms based on the DNA content and features at the breakpoints.

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Author information

Authors and Affiliations

  1. Ben May Department for Cancer Research, Department of Human Genetics, Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA

    Lixing Yang

Authors
  1. Lixing Yang
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Corresponding author

Correspondence to Lixing Yang .

Editor information

Editors and Affiliations

  1. Department of BioMedical Research, University of Bern, Bern, Switzerland

    Charlotte Ng

  2. Department of Biomedicine, University of Basel, Basel, Switzerland

    Salvatore Piscuoglio

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Yang, L. (2022). Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms. In: Ng, C., Piscuoglio, S. (eds) Variant Calling. Methods in Molecular Biology, vol 2493. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2293-3_8

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  • DOI: https://doi.org/10.1007/978-1-0716-2293-3_8

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2292-6

  • Online ISBN: 978-1-0716-2293-3

  • eBook Packages: Springer Protocols

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