Partek Flow Documentation

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Due to fundamental differences between the statistical models of employed by different variant detection tools, as well as different varying parameter optimizations within tools selected for unique detection 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 any all possible variants, whereas in other studies the goal is to generate a list of variants with increased confidence that they are 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 additional at least discrete variants node(s) exists in the project. The task will generate to two new variant data nodes and underlying vcf files, : one for the union and one for the intersection of the variant data (Figure 1).

 

 

Numbered figure captions
SubtitleTextGenerating data nodes from the combine Combine variants task
AnchorNamecombine variants pipeline

 

 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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Numbered figure captions
SubtitleTextSelecting a variant node for use in the combine Combine variants task
AnchorNamecombine variants dialog

 

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