How to run the InDels and Structural Variants tool

To start the structural variant detection:

        Toolbox | Resequencing (Image resequencing) | InDels and Structural Variants tool (Image structuralVariationDetection_16_n_p)

This will open up a dialog. Select the read mapping of interest as shown in figure 22.40 and click on the button labeled Next.

Image indels_and_structuralvariation_step2
Figure 22.40: Select the read mapping of interest.

The next wizard step (Figure 22.41) is concerned with specifying parameters related to the algorithm used for calling structural variants. The algorithm first identifies positions in the mapping(s) with an excess of reads with left (or right) unaligned ends. Once these positions and the consensus sequences of the unaligned ends are determined, the algorithm maps the determined consensus sequences to the reference sequence around other positions with unaligned ends. If mappings are found that are in accordance with a 'signature' of a structural variant, a structural variant is called. For further details about the algorithm see section 22.9.3.

Image indels_and_structuralvariation_step3
Figure 22.41: Select the relevant settings.

The 'Significance of unaligned end breakpoints' parameters are concerned with when a position with unaligned ends should be considered by the algorithm, and when it should be ignored:

The Calculation of unaligned end consensus parameters can improve the calculation of the unaligned end consensus by removing bases according to:

The 'Filter variants' parameters are concerned with the amount of evidence for each structural variant required for it to be called:

'Reference masking' allows specification of target regions:

Note! As the set of identified unaligned end breakpoints differs between runs where a target region track has been specified and where it has not, the set of predicted indels and structural variants is also likely to differ. This is because the indels and structural variants are predicted from the mapping patterns of the unaligned ends at the set of identified breakpoints. This is also the case even if you restrict the comparison to only involve the indels and structural variants detected within the target regions. You cannot expect these to be exactly the same but you can expect a large overlap.

Specify these settings and click Next. The "Results handling" dialog (Figure 22.42) will be opened. The Indels and Structural variants tool has the following output options:

Image indels_and_structuralvariation_step4
Figure 22.42: Select output formats.

An example of the output from the InDels and Structural Variant tool is shown in Figure 22.43. The output is described in detail in the next section (section 22.9.2).

Image standaloneVsTracks
Figure 22.43: Example of the result of an analysis on a standalone read mapping (to the left) and on a reads track (to the right).