HomeCLC FAQ - Analyses-related questionsVariant detection and reportingHow to add flanking sequence to variants in the CLC Genomics Workbench?

9.2. How to add flanking sequence to variants in the CLC Genomics Workbench?

There are two different ways in the CLC Genomics Workbench to add flanking sequences to variant information. The first option adds a column to the variant table, which shows the variant including the flanking sequence. The other option creates a new sequence list of the variants with flanking sequences.

The first better shows the flanking sequence in context with the variants. If you are going to do further analysis with the sequence information, or need to export it as a sequence list, the second option might be more suitable.  In many cases, it may suit the analysis requirements to run both tools.


Adding flanking information to the variant table

Go to the toolbox of the CLC Genomics Workbench:

Resequencing Analysis | Annotate and Filter Variants | Annotate with Flanking Sequence

In the wizard you first choose the variant track, in the next step you choose the reference track and flanking size that you would like to include.

This tool is described in our manual here:



Creating a sequence list with the flanking sequence (including the variant)

Go to the tool box of the CLC Genomics Workbench:

Classical Sequence Analysis | General Sequence Analysis | Extract Annotations

In the wizard you,

  • Select the variant track.
  • Then choose the reference sequence and the types of annotations that you would like to extract, i.e. SNV, MNV, Insertion, Deletion and/or Replacement. In this step you also choose the length of the flanking sequence. Using this option a different number of residues for the flanking sequence upstream and downstream can be selected.
  • Finally you choose how to name the new sequences. Here you need to make sure to include annotation region and chromosome, so that you can identify the variant later.

This tool is described in our manual here:


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