Join Nearby Variants

The Join Nearby Variants tool merges variants that are more than one nucleotide apart and within three nucleotides of each other into larger microhaplotypes. Because the tool merges variants regardless of their zygosity and frequency, it is most suited for use on isolates from monoploid organisms, such as most viruses and bacteria.

Merging variants allows amino acid changes to be more precisely determined by the Amino Acid Changes tool.

To run the tool, go to

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Drug Resistance Analysis (Image resistance_folder_closed_16_n_p) | Join Nearby Variants (Image join_nearby_var_16_n_p)

The tool takes a variant track as input.

The following parameters are available (figure 12.10):

Image joinnearbyvariantsdialog
Figure 12.10: Join Nearby Variants parameter settings.

Note: The Codon alignment option is primarily intended for matching variants against variant databases from outside the CLC Genomics Workbench. Databases of known variants (such as the WHO drug resistance variant database, Reference Data Elements), can have variants given as amino acid substitutions i.e., given in triplets/codon MNVs as opposed to larger substitutions, like when called within the CLC Workbench. These longer variants must be split on codon boundaries in order to accurately match the database when using Filter against Known Variants or Annotate from Known Variants.

Detailed behavior