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The task dialog for Annotate variants (SnpEff) contains two sections: Select SnpEff database and Advanced options (Figure 1). Select SnpEff database will specify the reference assembly to utilize for variant detection. 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^®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 to library files from within the task. Select SnpEff database will allow selection of databases utilized for prediction, and Partek ^® Flow ^® provides automated download of a limited number of these databases. Databases previously added to library files (see Library File Management) will be available for selection or Add SnpEff variant database in the menu can be utilized to import the reference sequence to library files from within the task. Additional information of SnpEff databases can be found in the SnpEff documentation.

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