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SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.

Jonathan R Belyeu1,2, Thomas J Nicholas1,2, Brent S Pedersen1,2

  • 1Department of Human Genetics, University of Utah, 15 S 2030 E, Salt Lake City, UT, USA.

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SV-plaudit is a novel framework for quickly curating structural variant (SV) predictions using cloud-based visualization and crowd-sourced evaluation. This tool aims to streamline variant calling pipelines and biological data curation.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Structural variants (SVs) are crucial in genomic research but challenging to accurately predict.
  • Existing methods for SV curation are often time-consuming and labor-intensive.

Purpose of the Study:

  • To introduce SV-plaudit, a framework designed for rapid and efficient curation of structural variant predictions.
  • To enable crowd-sourced evaluation of SV quality through a user-friendly web application.

Main Methods:

  • SV-plaudit generates images visualizing coverage and alignment signals for each SV across multiple samples.
  • These images are hosted on a cloud framework, accessible via a client-side web application for user assessment.
  • Curated reports can be exported as tab-delimited files or annotated Variant Call Format (VCF) files.

Main Results:

  • A proof-of-principle study demonstrated that nine researchers could evaluate 1,350 SVs each within one hour.
  • The framework facilitates rapid, collaborative assessment of SV prediction quality.

Conclusions:

  • SV-plaudit offers a scalable and efficient solution for structural variant curation.
  • The framework is expected to become a standard component in variant calling pipelines and for crowd-sourcing other biological data analyses.