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 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.

Selecting 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 transcript model (such as RefSeq). Annotation models previously added to library files (see Library File Management) will be available for selection or Add annotation model in the drop-down list can be utilized to import an 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, and this region will considered the promoter of a feature.

Selecting Annotate with known variants will provide the ability to specify a Variant annotation database (Figure 3). Known variant databases in vcf format, such as dbSNP¹ and 1000 Genomes² for human variants, can be used in the task. 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 employed 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 from within the task. 

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