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Setting up the task (Figure 1) involves identifying the Genome Build used for variant detection and the Sample to validate within the project.  Target specific regions allows for specification of the Target regions for this study, relating to the regions sequenced for all samples in the project.  Benchmark target regions represents the regions that have been previously interrogated to identify “gold standard” variant calls in the sample of interest.  These parameters are important to ensure that only overlapping regions are compared, avoiding the identification of false positives or false negative variants in regions covered by only the project sample or the “gold standard” sample.  Both sections utilize a Gene/feature annotation file, which can be previously associated with Partek^® Flow^® via Partek Flow via Library File Management or added on the fly. The Validated variants file is a single sample vcf file containing the “gold standard” variant calls for the sample of interest, and can be previously associated with Partek^® Flow^® Partek Flow as a Variant Annotation Database via Library File Management or added on the fly.

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