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Structural Variations

The "Somatic Structural Variations" and "Germline Structural Variations" sections contain the results of discovery of somatic and germline, respectively, long deletions, duplications, inversions, and translocations in the sample.

Somatic variations occur after conception and are not passed on to children. They can cause cancer or other diseases. Somatic variations discovery is carried out only for tumor tissue samples and, therefore, the results are presented only on the tumor tissue sample page.

Germline variations can be discovered in any cells of the body and are passed on from parents to offspring. Accordingly, germline variations discovery is carried out both for tumor tissue samples (in the case of single tumor tissue samples without control) and for non-tumor tissue samples. For a set of tumor/normal samples, the results of the germline variations discovery in the normal sample are presented on the pages of both samples of the set.

For a single tumor sample without control, the results of discovery of somatic and germline variations are combined into one section:

The detected and annotated structural variations are presented in all sections as:

  1. Text file in CSV (Comma-Separated Values) format. To download the file, click on .
  2. File in VCF 4.2 (Variant Call Format) format. To download the file, click on .
  3. File in Google Spreadsheet (only a limited number of variations can be shown). To open the file, click on .
  4. Integrative Genomics Viewer (IGV) is an embedded module for visualization of variations on the genome. To open the module, click on . To see simultaneously two border regions of the certain region in IGV, click on , and to return to the visualization of the entire region, click on . If you would like to go to the position opened in IGV in Decipher genome browser, click on .
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If you would like to add the track of annotated structural variations discovered in the sample analyzed by Genomenal to IGV desktop application, you can load it via URL. To do this, do the following:

  1. Right-click on and select the "Copy link address" option.
  2. Load the track via URL to the IGV desktop application as described here.
  3. Open the "Workflow details" tab on the sample page and expand the details of the "Structural variations discovery" stage for a sample uploaded in FASTQ format, or the "SV annotation" stage for a sample uploaded in VCF format, and then expand the details of the "Annotate SV VCF" task. Right-click on the link to the annotation index file "Download Filtered variants VCF_TBI" and select the "Copy link address" option.
  4. Add the index file URL in the corresponding field in IGV.
  5. Click "OK". Done! The track of annotated variations discovered in the sample has been added to IGV.