Combine Variants

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).

Figure 1. Generating data nodes from the Combine variants task

To run the task, select a Variants data node and then click the Combine variants from the task menu. The task dialog (Figure 2) will allow you to select a second Variants data node to be combined with the first. The selection allows for only one other data node to be used in the task. If there are no other valid variant tasks available within the project, a message stating "No connections to upstream task found" will be displayed.

Figure 2. Selecting a variant node for use in the Combine variants task

Currently, this is the only task in Partek Flow that requires two input data nodes and then generates two output data nodes.

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