TruSight Software includes an Integrative Genomics Viewer (IGV). You can use IGV to view variant details across all tabs and compare data with variants called in the same case or noted in other databases.
IGV supports creating virtual variants when viewing data at the variant level. For more information, see Virtual Variants.
Reference Tracks
IGV displays the following reference data set tracks.
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Ensembl genes
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RefSeq genes
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ISCA benign
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ISCA uncertain
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ISCA pathogenic
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CNV population depth
CNV population depth is supported for GRCh38 only.
Sample Tracks
IGV displays the following sample tracks. The IGV Track Settings option lists source files for the tracks.
A single sample is represented from the joint genotyped small variant VCF.
Structural Variants
Structural variants.
VCF/BAM
Visualization of sequencing read coverage and raw read reference-alignments for each subject in the case.
Visualize Data
1.
To display the data in IGV, perform one of the following actions:
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To view data at the variant level, select the IGV column entry for the variant.
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To view data at the case level, select Case Visualization above the grid.
The IGV visualization is displayed in a new browser tab.
2.
To display data for a local file, select Local File, and then navigate to an IGV-formatted file. Large files must be compressed before uploading. For more information, see Custom IGV Files.
Large visualization files must be compressed before upload.
3.
To view reference tracks, select IGV Track Settings, and then select the checkboxes for the tracks or group of tracks you want to view.
4.
[Optional] View breakends. The breakend view zooms in on the ends of breakpoints in the sequence.
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To visualize breakends in separate views, select View Breakends.
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To return to a single breakend view, select Join Breakends.
5.
[Optional] Select Add New Comment to add or update a comment about the variant.
Each new or updated IGV comments is copied as a separate entry to the Variant Details tab comments for the variant.
The Variant Details tab does not indicate the source of comments. To differentiate entries created in IGV, preface comments with or other short identifier.
6.
Use the following options to interact with the visualization.
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Zoom into an area of interest.
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Pan the visualization by clicking and dragging or by selecting the left and right arrows on the karyogram.
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Select an item in the visualization to view additional information about the item.
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Show or hide IGV elements.
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Karyotype Panel
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Track Labels
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Center Line
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Cursor Guide
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Change track settings.
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Set track name
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Set track height
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Collapse, squish, or expand exon rows
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Remove track
The gene model display track reflects the transcript reference standard (Ensembl or Refseq) specified in Settings.
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