- The tool will detect NO structural variants if there are NO reads with unaligned ends in the read mapping.
- Read mappings made with the CLC 'Map reads to reference' tool with the 'global' option switched on will have NO unaligned ends and the Structural Variation 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 Mapper are NOT optimal for the detection of structural variants with this tool. This is due to the fact that, the Large Gap Read Mapper will map some reads with (large) gaps, that would be mapped with unaligned ends with standard read mappers, and thus will leave a weaker unaligned end signal in the mappings for the Structural Variation tool to work with.
In it's current version the InDels and Structural Variants tool has the following known limitations:
- It will only detect intra-chromosomal structural variants.
- There is no reporting of the zygosity of the detected structural variants (there is, however, a 'variant ratio' (explained under 'Add information regarding 'zygosity'' in Procedure for inspecting breakpoint signatures and inferring Structural Variants), which can be used as a guidance for zygosity).
- The Structural Variation algorithm
- Creating Left- and Right breakpoint signatures
- Predicting Structural Variants