skip to main content
Roche logo
2. GS Reference Mapper : 2.10 Using the Variants Tab : 2.10.3 The HC Structural Variants Sub-Tab
2.10.3
The HC Structural Variants Sub-Tab
The HC Structural Variants sub-tab (Figure 65) shows locations of larger-scale changes relative to the reference that are indicated by a group of reads. Entries in the table are classified as either Rearrangement points or Rearrangement regions. See Section 2.17.1.15 for more details on these topics. Right-clicking on a row opens a contextual menu from which one can access the alignment that underlies the variation. Pausing the mouse over a row displays a tooltip providing information about that variation.
A
 
B
Figure 65: gsMapper Variants tab, HC Structural Variants sub-tab. A: Left columns; B: Right columns.
 
Note on handling Paired End reads when computing Structural Variants:
 
The detection of Rearrangement Regions depends on finding clusters of Paired End reads considered to be False Pairs. When Paired End libraries using different span distances are used (e.g. 3kb and 8kb or 20kb libraries), more than one cluster may be found for the same structural variation.