Remove Reference Variants

This tool has been deprecated and will be retired in a future version of the software. It has been moved to the Legacy Tools (Image legacy_tools) folder of the Toolbox, and its name has "(legacy)" appended to it. If you have concerns about the future retirement of this tool, please contact QIAGEN Bioinformatics Support team at

The variant tracks produced by the variant detection tools of CLC Genomics Workbench include reference alleles complementing a non-reference allele (i.e. a heterozygous variant where only one allele is different from the reference). In some situations, this information is not necessary, and these reference allele variants can be filtered away.

        Legacy Tools | Remove Reference Variants

This opens a dialog where you can select a variant track (Image variant_track_16_n_p) that should be filtered.

Click Next and Finish to create a new track without the reference variants.

For removing reference variants whose alternate allele has already been filtered, use the tool Remove Homozygous Reference Variants. It is also possible to configure Filter on Custom Criteria with a criteria set to "Reference allele = No" to mimic the functionality of Remove Reference Variants.