Output from the Structural Variant Caller

The tool produces the following outputs: The indels variant track, and the inversions and long indels annotation tracks can be exported to VCF.

The reason for putting the indels larger than 100,000 bp in a separate annotation track, is that the very long variants have very long either allele or reference entries in the variant track are challenging to work with in the track viewer.

Indels variant track

The indels track contains all the standard variant annotations, except for the "Probability" and "QUAL" columns which are only preduced when the Whole genome Sequencing application is chosen. When produced, the content of the "Probability" column is the average of the probabilities of the breakpoints used to infer the feature, and the content of the "QUAL" column is the Phred score version of that probability.

As the indels are inferred indirectly from the unaligned ends, and hence are not necessarily directly visible within the aligned parts of the reads, the indel variant annotations are approximated from the breakpoints and the unaligned ends of reads in the read mapping. Figure 11.19 shows a read mapping of a 52bp deletion and the read mapping in which it was inferred by examination of the indirect evidence in the reads with unaligned ends, along with the approximated variant annotations (e.g count, coverage and frequency).

Image structvar_deletionIndirectEvidence
Figure 11.19: A 52 bp deletion with approximated variant annotations and the read mapping in which it was inferred.

In addition to the standard variant annotations, the indel track contains the following columns with characteristics of the inferred structural variant (figure 11.20):

Image structvar_indelstrack
Figure 11.20: The Structural Variant Caller indels track.

Long indels and inversions annotation tracks

The long indels and inversions feature tracks contain the same columns as the indels track, except that the "Type", "Reference", "Allele" and "Reference allele" columns in the indels track are replaced by a single "Name" column in the feature track. The "Name" column specifies whether the feature is a deletion, insertion or inversion.

The report

The report (figure 11.21) gives an overview of the numbers and types of structural variants found in the sample.

Image structvar_report
Figure 11.21: The Structural Variant Caller report.

It contains:

Breakpoint track (BP)

The breakpoint track (figure 11.22) contains a row for each called breakpoint with the following information

Image structvar_breakpoints
Figure 11.22: The Structural Variant Caller breakpoints track.