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Loss of reference allele information for neighboring SNPs when using certain downstream filtering tools after variant calling

An issue was discovered where multiple nucleotide variants (MNV) representing a reference allele would be filtered out when any of the filtering tools listed below was used.

As a consequence of this problem, the number of reads reported as supporting the reference allele could be incorrect after filtering was carried out. If the output was then exported, e.g. to VCF, the incorrect counts would also be exported.

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

Software affected

List of tools that cause the described behavior


CLC Genomics Workbench


Biomedical Genomics Workbench

  1. Annotate with Overlap Information
  2. Annotate with Flanking Sequences
  3. Annotate with Exon Numbers
  4. Compare Variants within Group
  5. GO Enrichment Analysis
  1. Add Information from Overlapping Genes
  2. Add Flanking Sequences
  3. Add Exon Numbers
  4. Compare Shared Variants in a Group of Samples