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.

Original languageEnglish
Title of host publicationNeuromethods
PublisherHumana Press Inc.
Number of pages14
StatePublished - 2022

Publication series

ISSN (Print)0893-2336
ISSN (Electronic)1940-6045


  • Long-reads
  • NGS
  • Neurodegeneration
  • Pipeline
  • Snakemake
  • Structural variation


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