The InDels and Structural Variants tool is designed to identify structural variants such as insertions, deletions, inversions, translocations and tandem duplications in read mappings. The tool relies exclusively on information derived from unaligned ends (also called 'soft clippings') of the reads in the mappings. This means that:
- The tool will detect NO structural variants if there are NO reads with unaligned ends in the read mapping.
- Read mappings made with the Map Reads to Reference tool with the 'global' option switched on will have NO unaligned ends and the InDels and Structural Variants tool will thus find NO structural variants on these. (The 'global' option means that reads are aligned in their entirety - irrespectively of whether that introduces mismatches towards the ends of the reads. In the 'local' option such reads will be mapped with unaligned ends).
- Read mappings based on really short reads (say, below 35 bp) are not likely to produce many reads with unaligned ends of any useful length, and the tool is thus not likely to produce many structural variant predictions for these read mappings.
- Read mappings generated with the Large Gap Read Mapping tool of the Transcript Discovery plugin are NOT optimal for the detection of structural variants with this tool. This is because this tool will map some reads with (large) gaps that would be mapped with unaligned ends with standard read mappers. This results in a weaker unaligned end signal in these mappings for the InDels and Structural Variants tool to work with.
In its current version the InDels and Structural Variants tool has the following known limitations:
- It will only detect intra-chromosomal structural variants.
- Run the InDels and Structural Variants tool
- The Structural Variants and InDels output
- The InDels and Structural Variants detection algorithm
- Theoretically expected structural variant signatures
- How sequence complexity is calculated