Advanced Structural Variant Detection

To run the Advanced Structural Variant Detection (beta) tool:

        Toolbox | Resequencing Analysis (Image resequencing) | Variant Detection (Image variant_detection_folder_closed_16_h_p) | Advanced Structural Variant Detection (Image structural_variation_detection_16_n_p)

Once the tool wizard has opened (figure 2.1), choose the input you would like to use. The Advanced Structural Variant Detection tool accepts read mappings as either reads tracks or stand-alone read mappings.

Image advstrucvardet1
Figure 2.1: Select one or several reads tracks or stand-alone read mappings.

The tool has the following options (figure 2.2):

Image advstrucvardet2
Figure 2.2: Set the model parameters for the tool.

The tool outputs a report, a Breakpoint track (BP), and 2 Variant track (SV) and (SV annotations)

The report

The report (figure 2.3) gives an overview of the numbers and types of structural variants found in the sample.

Image advstrucvardet_report
Figure 2.3: The Advanced Structural Variant Detection (beta) report.

It contains:

Breakpoint track (BP)

The breakpoint track (figure 2.4) contains a row for each called breakpoint with the following information

Image advstrucvardet_bptrack
Figure 2.4: The Advanced Structural Variant Detection (beta) breakpoint track.

Variant track (SV) and Variant as annotation track (SV annotations)

The variant tracks (figure 2.5) contain a row for each of the called structural variations. In the case of the annotated track, the structural variations are stored as annotations: large deletions may be easier to visualize in this format.

Image advstrucvardet_variantstrack
Figure 2.5: The Advanced Structural Variant Detection (beta) variant track.

In addition to the regular variant tracks information, the variant table contains the following information: