Variant Review with the Integrative Genomics Viewer (IGV)
By James T. Robinson, Helga Thorvaldsdóttir, Aaron M. Wenger, A. Zehir, Jill P. Mesirov. Cancer Research, 2017
957 citations recorded by the source corpus.
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 (SNV) and structural variants (SV), with examples from both cancer and germline datasets. IGV is freely available at https://www.igv.org.
Subfields: Cancer Research, Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/05c376a55c31b6199b6bdf995d54635c00043733
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Cancer Research
- James T. Robinson
- Jill P. Mesirov
- Douglass Turner
- Helga Thorvaldsdóttir
- David Haussler
- Robert C. Edgar
- Steven Henikoff
- Daniel C. Koboldt
In Genetics
- Adam M. Phillippy
- Anton I. Korobeynikov
- Evan E. Eichler
- Shilpa Garg
- David Haussler
- Tobias Marschall
- Jillian F. Banfield
- Benedict Paten
In Molecular Biology
- Adam M. Phillippy
- Helga Thorvaldsdóttir
- Anton I. Korobeynikov
- Jill P. Mesirov
- Douglass Turner
- James T. Robinson
- Dmitry Meleshko
- Evan E. Eichler
Citations in the corpus
- A draft human pangenome reference (2022, background): “(Supplementary Figure 43) shows a snapshot of the IGV browser (Robinson et al., 2017) illustrating the coverage of the adapter-containing reads along the genome.”
- igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) (2020, background): “A particular strength of IGV is manual review of genome variants, both single-nucleotide and structural variants [7].”
- Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “DARTH generates these files so that the can be easily loaded into a genome browser such as JBrowse 78 or IGV 79 .”