Home → CLC software: Important notifications → Issues affecting only older versions of products → Loss of reference allele information for neighboring SNPs when using certain downstream filtering tools after variant calling
2.9. 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.
- CLC Genomics Workbench 6.0.4 to 12.0
- CLC Genomics Server 5.0.4 to 11.0
- All versions of Biomedical Genomics Workbench
List of tools that cause the described behavior
CLC Genomics Workbench
Biomedical Genomics Workbench