The Annotate variants task in Partek^® Flow^® provides a means to add information with regards to genomic features, such as transcript models, and existing variant databases to the variants contained in the projects.   This information can be useful for filtering, interpreting, and prioritizing variants for downstream investigation.  The Annotate variants task can be invoked from any Variants or Annotated variants data node, and the task will be added to and supplement any existing annotation in the underlying vcf files.  Annotation information will also be visible in the View variants Variant report and the Summarize cohort mutations Cohort mutation summary report.  

 Annotate Annotate variants dialog

The task dialog for Annotate variants contains three sections:  Assembly, Annotate with genomic features, and Annotate with known variants (Figure 1).  If variant detection was performed in Partek^® Flow^®, the Assembly will be displayed as text in the section, and you do not have the option to change the reference.  In the event that variant detection was performed outside of Partek^® Flow^®, you will need to select the appropriate Assembly utilized for variant detection in the drop-down list.  Assemblies previously added to library files (see Library File Management) will be available for selection or New assembly… can be utilized to import the reference sequence from within the task.

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