The Structural Variants and InDels output

The Structural Variants and InDels report

The report gives an overview of the numbers and types of structural variants found in the sample. It contains

The Breakpoints track (BP)

The breakpoints track contains a row for each called breakpoint with the following information:

Note that typically, breakpoints will be found for which it is not possible to infer a structural variant. There may be a number of reasons for that: (1) the unaligned ends from which the breakpoint signature was derived might not be caused by an underlying structural variant, but merely be due to read mapping issues or noise, or (2) the breakpoint(s) which the detected breakpoint should have been matched to was/were not detected, and therefore no matching breakpoint(s) were found. Breakpoints may go un-detected either because of lack of coverage in the breakpoint region or because they are located within regions with exclusively non-uniquely mapped reads (only unaligned ends of uniquely mapping reads are used).

The InDel variant track (InDel)

The Indel variant track contains a row for each of the called insertions or deletions (see section [*] for a description of the variant types Insertion and Deletion). These are the small to medium sized insertions, as well as deletions up to 200 bp in length, for which the algorithm was able to identify the allele sequence, i.e., the exact inserted or deleted sequence.

For insertions, the full allele sequence is found from the unaligned ends of mapped reads. For some insertions, the length and allele sequence cannot be determined and as these do not fulfill the requirements of a 'variant', they do not qualify for representation in the InDel Variant track but instead appear in the Structural Variant track (see below).

The information provided for each of the indels in the InDel Variant track is the 'Chromosome', 'Region', 'Type', 'Reference', 'Allele', 'Reference Allele', 'Length' and 'Zygosity' columns that are provided for all variants (see section 26.6.1). Note that the Zygosity field is set to 'Homozygous' if the 'Variant ratio' is 0.80 or above, and 'Heterozygous' otherwise.

In addition, the track provides the following information, primarily to assess the degree of evidence supporting each predicted indel:

The Structural Variant track (SV)

The Structural Variant track contains a row for each of the called structural variants that are not already reported in the InDel track. It contains the following information: