HomeCLC software: Important notificationsIssues affecting only older versions of productsRead counts reported for contained multi-nucleotide variants (MNVs) are too low under certain circumstances

2.29. Read counts reported for contained multi-nucleotide variants (MNVs) are too low under certain circumstances

Under certain limited circumstances, the read count reported for the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools is lower than it should be.

This issue affects a small subset of variants where all the following apply:

  • there are reads suggesting the presence of a large MNV or deletion and reads suggesting the presence of smaller MNVs within the larger variant region, AND
  • the smaller, contained MNVs have a different sequence than the larger variant, AND
  • one or more of the potential variants of that region are disregarded during variant calling process and reads from the disregarded variants are reassigned to potential variants still under consideration that they support, AND
  • a potential variant supported by these reassigned reads is then also disregarded.

In such a situation, the initially reassigned reads should be checked again for support of potential variants still under consideration. However, in affected software versions, this second round of checks is not done.

Thus, under this set of circumstances, the count reported for a variant can be lower than it should be.

We expect this issue to affect very few variants and to have limited impact for those affected. However, some false negatives may be present in affected software versions: Some MNVs fitting the description above, which are supported by reads initially allocated to other potential variants, might pass count or frequency filters that they currently do not, including filters within the variant callers themselves, if this problem were not present.

Software affected

  • From CLC Genomics Workbench 7.5 up to and including version 9.5.4. Also affects version 10.0 and 10.0.1.
  • From Biomedical Genomics Workbench 2.1 up to and including version 3.5.4. Also affects version 4.0.
  • From CLC Genomics Server 6.5 up to and including version 8.5.4. Also affects version 9.0.

This issue was fixed in the following versions. Later releases in the same major version line (e.g. 9.x, 4.x, etc.) also contain the fix.

  • CLC Genomics Workbench 9.5.5
  • CLC Genomics Workbench 10.1
  • Biomedical Genomics Workbench 3.5.5
  • Biomedical Genomics Workbench 4.1
  • CLC Genomics Server 8.5.5
  • CLC Genomics Server 9.1

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