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Cancer Res. 2017 Nov 1;77(21):e31-e34. doi: 10.1158/0008-5472.CAN-17-0337.

Variant Review with the Integrative Genomics Viewer.

Author information

1
School of Medicine, University of California San Diego, La Jolla, California. jrobinso@ucsd.edu.
2
Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
3
Pacific Biosciences, Menlo Park, California.
4
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
5
School of Medicine, University of California San Diego, La Jolla, California.
6
Moores Cancer Center, University of California San Diego, La Jolla, California.

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 Cancer Res; 77(21); e31-34. ©2017 AACR.

PMID:
29092934
PMCID:
PMC5678989
DOI:
10.1158/0008-5472.CAN-17-0337
[Indexed for MEDLINE]
Free PMC Article

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