HomeCLC software: Important notificationsIssues affecting only older versions of productsInDels and Structural Variants tool produces additional breakpoints if broken pairs included

2.27. InDels and Structural Variants tool produces additional breakpoints if broken pairs included

Issue Description

Additional breakpoints can be reported by the InDels and Structural Variants tool when both, broken and intact reads, map to a given region. This issue only affects analyses where the option Ignore broken pairs is unchecked and when using one of the affected software versions. By default Ignore broken pairs is checked.

Expected Impact

  • Variants affected are reported as "complex" variants, and are included in the Structural Variants (SV) track instead of the Indel Variants (InDel) track output by the InDels and Structural Variants tool.
  • Any tool that uses an affected InDel track thus also has the potential to be affected via knock-on effects of any missing insertion or deletion entries.

    For example,
    • If an affected InDel track is used as a guidance track for the Local Realignment tool, then for regions where indels are not present due to this issue, but should be, the Local Realignment mapping output could be affected.
    • If an affected mapping were then used as input to Basic Variant Detection, Fixed Ploidy Variant Detection or Low Frequency Variant Detection tool, indels affected by this issue may then also be missed by the variant detection tools, despite the existence of reads supporting them in the data.



If working with software affected by this issue, please choose to keep the Ignore broken reads option checked when running the InDels and Structural Variants tool.

Affected Software

  • CLC Genomics Workbench 9.5 through 9.5.5, and versions 10.0 through 10.1.1
  • Biomedical Genomics Workbench 3.5 through 3.5.5, and versions 4.0 through 4.1.1
  • CLC Genomics Server 8.5 through 8.5.5, and versions 9.0 through 9.1.1

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