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Variant Review with the Integrative Genomics Viewer

Cancer Research · 2017 · Vol. 77(21) · pp. e31–e34

James Robinson✉Helga ThorvaldsdóttirAaron M. WengerAhmet ZehirJill P. Mesirov(University of California, San Diego)

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 examples from both cancer and germline datasets. IGV is freely available at https://www.igv.org <i>Cancer Res; 77(21); e31-34. ©2017 AACR</i>.

Genomics and Phylogenetic Studies Cancer Genomics and Diagnostics Genomics and Rare DiseasesVisualizationGenomicsComputer scienceComputational biologyFalse positive paradoxSet (abstract data type)DNA sequencingInterpretation (philosophy)Data setData science

MeSH terms

HumansNeoplasmsSoftwareSequence AlignmentSequence Analysis, DNAComputational BiologyPolymorphism, Single NucleotideGenomicsHigh-Throughput Nucleotide Sequencing