The Annotate variants task in Partek^® Flow^® provides a means to add information with regards to genomic features, such as transcription models, and existing variant databases to the variants contained in the projects vcf files.   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 supplement any existing annotation in the vcf file.  Annotation information will also be visible in the View variants Variant report and the Cohort mutation summary.  

 Annotate variants dialog

The task dialog for Annotate variants contain three sections:  Assembly, Annotated with genomic features, and Annotate with known variants (Figure 1).  If the 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.  Assemblies previously added to library files (see Library File Management) will be available for selection or New assembly… in the menu can be utilized to import the reference sequence to library files within the task.

Selecting the Annotate with genomic features provides the means to add Gene/feature information to the variants (Figure 2).  This typically takes the form of overlaying a transcription model (such as RefSeq Transcripts) or amplicon information.  Annotation models previously added to library files (see Library File Management) will be available for selection or Add annotation model in the menu can be utilized to import the annotation model to library files within the task.  Promoter upstream limit and Promoter downstream limit provides a means to set the number of bases flanking the transcription start site that will considered the promoter region.

Selecting Annotate with known variants will provide the ability to specify a Variant annotation database (Figure 3).  These vcf files derived from known variant databases, such as dbSNP¹ and 1000 Genomes².  Additional databases not provided for automated download in Partek^® Flow^®, such as the Catalogue of Somatic Mutations in Cancer (COSMIC)³, can be obtained and imported by the user.  Variant databases previously added to library files (see Library File Management) will be available for selection or Add variant database in the menu can be utilized to import the variant database to library files within the task. 

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