articleCancer ResearchOct 31, 2017GREEN OA

Variant Review with the Integrative Genomics Viewer

JRJames RobinsonHTHelga ThorvaldsdóttirAMAaron M. WengerAZAhmet ZehirJPJill P. Mesirov

University of California San Diego · Broad Institute · +2 more institutions

PubMed
Indexed incrossrefpubmed

Abstract

Abstract Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and interpretation of NGS datasets, as well as other types of genomic data. Here, we present a short overview of IGV's variant review features for both single-nucleotide variants and structural variants, with…

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Topics & keywords

Topics
Keywords
  • Visualization
  • Genomics
  • Computer science
  • Computational biology
  • False positive paradox
  • Set (abstract data type)
  • DNA sequencing
  • Interpretation (philosophy)
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