Copy Number Variant Detection (CNVs) can give wrong results when targets overlap and coverage tables are used as controls

Issue description

The Copy Number Variant Detection (CNVs) tool can generate incorrect fold change estimates when:

• There are overlapping targets in the target regions track, and
• The “Merge overlapping targets” option is enabled, and
• A coverage table generated by QC for Targeted Sequencing is provided as the control mapping.

QIAGEN reference target tracks do not contain overlapping regions, thus analyses using these are not affected by this problem.

Recommendations

We recommended re-running all potentially affected analyses, providing a read mapping as the control mapping instead of a coverage table generated by QC for Targeted Sequencing.

Affected software

• QIAGEN CLC Genomics Workbench 22.0 through 23.0.4
  QIAGEN CLC Genomics Server 22.0 through 23.0.4

  This issue was addressed in version 23.0.5.