Annotate Structural Variants
The main purpose of the Annotate Structural Variants tool is to calculate and add Count, Coverage and Frequency annotations to structural variants from InDel tracks detected by the InDels and Structural Variants tool.
The following tracks are taken as inputs:
- An InDel track. An output from the InDels and Structural Variants tool
- A Breakpoint track. An output from the InDels and Structural Variants tool
- A reads track. The read mapping used as input to the InDels and Structural Variants tool that led to the generation of the two tracks mentioned above.
These are used in the calculation and for further annotation of the resulting variant track. The Count, Coverage and Frequency are calculated as follows:
- Count The number of reads supporting the variant detected by the InDels and Structural Variants tool.
- Coverage The number of reads that overlap one or more relevant positions in the read mapping. "Relevant positions" here are the bases before and after the start and the end of the structural variant, and the bases before and after the breakpoints defining the structural variants.
- FrequencyThe number of reads in the mapping supporting the variant (Count) divided by the number of reads covering the relevant positions in the mapping, as defined above (Coverage).
Variants that are of the same type (SNV, MNV, insertions or deletions) are collapsed into a single variant if the breakpoints supporting the variant are within 20 bp and the calculation is performed on the consolidated variant.
Coverage for tandem duplications:Tandem duplications are insertions. For coverage of insertions, the reads overlapping the two positions before and after the insertion are considered. One breakpoint is the same as the insertion and so no new information is derived from this. The other breakpoint is at the other end of the detected duplicated interval, adding two relevant positions (before and after this breakpoint). So, for example, the coverage of a tandem duplication of length 40 at position 100 would be the number of mapped reads overlapping one or more of the following positions: 99, 100, 139, and 140.
Annotations from the Breakpoint track that are added to the variants are: p-value, Unaligned, Unaligned length, Perfect mapped, Not perfect mapped and Ignored mapped.
To run the Annotate Structural Variants tool, go to:
Toolbox | Biomedical Genomics Analysis () | Biomedical Utility Tools () | Annotate Structural Variants ()
The Annotate Structural Variants tool generates a variant track containing the same variants as the original InDel track with Count, Coverage, Frequency, and additional annotations taken from the Breakpoint track.