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The Filter variants task dialog can contains contain two to five sections, dependent on the variant caller used for detection and the level of annotation (Figure 1).  All instances of the task will include the following: Include region overlapping variants and a section for Quality.

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Selecting Include region overlapping variants will bring up a dialog to include variants located within genomic regions of interest (Figure 2), which could be regions such as transcript models or amplicons.    If 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 to library files from within the task.  The Gene/feature section will allow for the use of any annotation model specified in the library files (see Library File Management) in the drop-down menu or can be imported from within the task by selecting Add annotation model. If an annotation that contains gene-level information is selected, this filter will include both intronic and exonic regions.  

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