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snakeSV: Flexible Framework for Large-Scale SV Discovery

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Genomic Structural Variants in Nervous System Disorders

Part of the book series: Neuromethods ((NM,volume 182))

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Abstract

We present snakeSV, an open-source fast and scalable framework to analyze genomic structural variation (SV) at scale. The framework is easily deployable using Bioconda and can leverage cluster environments to speed up data processing via parallelization. Providing a set of preconfigured tools, all available at the Bioconda channel for easy installation, snakeSV combines a set of auxiliary scripts that makes it easy to integrate novel tools and features. Execution starts with one or many BAM files and produces a VCF file with SVs detected and jointly genotyped across samples and a report with relevant annotations. We also present two use cases to illustrate the pipeline features to improve SV discovery by using a panel of high-quality SVs and incorporating custom annotations to help biological interpretation.

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Author information

Authors and Affiliations

  1. Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Ricardo A. Vialle & Towfique Raj

  2. Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Ricardo A. Vialle & Towfique Raj

  3. Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Ricardo A. Vialle & Towfique Raj

  4. Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Ricardo A. Vialle & Towfique Raj

Authors
  1. Ricardo A. Vialle
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  2. Towfique Raj
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Corresponding authors

Correspondence to Ricardo A. Vialle or Towfique Raj .

Editor information

Editors and Affiliations

  1. Queen Square Institute of Neurology, University College London, London, UK

    Christos Proukakis

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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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Vialle, R.A., Raj, T. (2022). snakeSV: Flexible Framework for Large-Scale SV Discovery. In: Proukakis, C. (eds) Genomic Structural Variants in Nervous System Disorders. Neuromethods, vol 182. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2357-2_1

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  • DOI: https://doi.org/10.1007/978-1-0716-2357-2_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2356-5

  • Online ISBN: 978-1-0716-2357-2

  • eBook Packages: Springer Protocols

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