Annotating from known variants

Filter against known variants describes how to filter against known variants, but the CLC Genomics Workbench also includes a tool to annotate from known variants:

To run the Annotating from known variants tool, go to:

        Toolbox | Resequencing (Image resequencing) | Annotate and Filter | Annotate from Known Variants

This tool will create a new track with all the experimental variants including added information about overlapping variants found in the track of known variants. The annotations are marked in three different ways:

Exact match
This means that the variant position and allele both have to be identical in the input and the known variants track (however, note the extra option for joining adjacent SNVs and MNVs described below).
Partial MNV match
This applies to MNVs which can be annotated with partial matches if an SNV or a shorter MNV in the database has an allele sequence that is contained in the allele sequence of the annotated MNV.
This will report if the known variant track has an overlapping variant.

For exact matches, all the information about the variant from the known variants track is transferred to the annotated variant. For partial matches and overlaps, the information from the known variants are not transferred.