IGV Visualizations
BaseSpace Variant Interpreter includes an embedded Integrative Genomics Viewer (IGV). You can use IGV to view variant details across all tabs and compare it with variants called in the same case or noted in other databases.
To display the variant in IGV, select View in IGV from the Variant column of the Variant Grid. The IGV visualization is displayed in a new browser tab. 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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Select the track settings icon to change the track view. |
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Collapse, squish, or expand exon rows |
NOTE
The gene model display track reflects the transcript reference standard (Ensembl or Refseq) specified in Settings.
IGV Legend
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CNV
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Copy number variants are represented by the following colored lines. In cancer samples, the copy number gain and loss colors are reversed compared to germline samples.
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Grey—Copy neutral loss of heterozygosity |
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Pink—Non-specified copy number variation |
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Cancer sample (Tumor-only or Tumor-Normal )
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Structural Variants
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Structural variants are represented by the following colored lines.
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Blue-green—Tandem duplication |
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Green—Translocation breakend |
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