Variant Density (Variation) Not Plotted In Circular Genomic Viewer
(Doc ID 2317360.1)
Last updated on DECEMBER 05, 2019
Applies to:Oracle Healthcare Translational Research - Version 3.1 and later
Information in this document applies to any platform.
Variant Density ("Variation") is not plotted in Circular Genomic Viewer:
When selecting a patient with genomic data and go to circular Genomic Plot, the plot only shows the Karyotype bands, even though 'Sequence Variant Density' is selected.
The issue can be reproduced at will with the following steps:
1. Login to Cohort Explorer
2. Go to "Single Patient Viewer"
3. Select a patient with genomic data by name (e.g. 1008)
4. Under "Genomic Data", check "Specimen with Genomic Results"
5. Select the "Assembly Version" (e.g. GRCh37)
7. Under "Specimen For Result Types", click on the "SpecimenNumber" link (e.g. 118)
8. "Circular Genomic Viewer" page is displayed with Specimen ID, Patient ID, Specimen Type, Anatomical Site, Assembly Version already filled-in
9. Under "Specimen for Result Types", check "Sequence Variant Density"
10. Click on "Plot Graph" button
11. The graph is displayed containing ONLY "Karyotype Bands" information
Both "Karyotype Bands" and "Variation" should be listed on the plot.
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