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

Gigascience. 2018 Jul 1;7(7):giy064. doi: 10.1093/gigascience/giy064.

Abstract

SV-plaudit is a framework for rapidly curating structural variant (SV) predictions. For each SV, we generate an image that visualizes the coverage and alignment signals from a set of samples. Images are uploaded to our cloud framework where users assess the quality of each image using a client-side web application. Reports can then be generated as a tab-delimited file or annotated Variant Call Format (VCF) file. As a proof of principle, nine researchers collaborated for 1 hour to evaluate 1,350 SVs each. We anticipate that SV-plaudit will become a standard step in variant calling pipelines and the crowd-sourced curation of other biological results.Code available at https://github.com/jbelyeu/SV-plauditDemonstration video available at https://www.youtube.com/watch?v=ono8kHMKxDs.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • False Positive Reactions
  • Genetic Variation
  • Genome, Human
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Internet
  • Medical Informatics / methods*
  • Sequence Alignment*
  • Sequence Analysis, DNA*
  • Software