HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Marginally higher counts reported for a small subset of variants

3.2. Marginally higher counts reported for a small subset of variants

The count and read count values reported by the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools were found to be marginally higher than was actually the case for a small minority of cases.

We expect the issue described here to have little or no impact on the identification or interpretation of variant calls within the Workbench.

The issue described here has been fixed for the

  • CLC Genomics Workbench 9.5.4
  • Biomedical Genomics Workbench 3.5.4 and
  • CLC Genomics Server 8.5.4

These versions were released on February 14, 2017.

Issue details

This issue involves potential variants that overlap, where one of the overlapping variants, but not the other, is confirmed and reported as a variant in the results.

The consequences of this issue are, for the small group of affected variants:

  • Slightly higher variant frequencies could be reported than should have been. For some cases this could result in allele frequencies above 100% being reported.
  • Using software where this issue has been fixed could result in a small decrease in the final number of variants reported when compared to results reported using earlier versions. This would be due to some potential variants no longer passing the count, read count or allele frequency filtering constraints set. To give an idea of the magnitude of the change that one might observe: in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after the fix to this issue was implemented.

Software affected

  • CLC Genomics Workbench 7.5 up to and including version 9.5.3
  • Biomedical Genomics Workbench 2.1 up to and including version 3.5.3
  • CLC Genomics Server 6.5 up to and including version 8.5.3


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