Due to fundamental differences between the statistical models employed by different variant detection tools, as well as varying parameter optimizations within tools selected for discrete discovery goals, there can be a large number of unique and common variants identified between each instance of variant detection.  In some cases the goal of the study is to provide a list of all possible variants, whereas in other studies the goal is to generate a list of variants with increased confidence of true polymorphic sites.  To facilitate both possible goals, Partek^® Flow^® provides a Combine variants tool to generate either the union or intersection of two variants data nodes.  This task provides a means to identify common and unique variant calls in samples that have undergone two discrete variant calling tasks.  The Combine variants task can be invoked from any Variants or Annotated variants data node, assuming at least discrete variants node(s) exists in the project. The task will generate two new variant data nodes and underlying vcf files: one for the union and one for the intersection of the variant data (Figure 1).

 Combine variants dialog

The dialog for the Combine variants task will provide a list of other discrete variant data nodes within the project, and selection allows for only one node to be utilized in the task (Figure 2).

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