Validate variants is available for data nodes containing variants (Variants, Filtered  variants, or Annotated Variants).  The purpose of this task is to understand the performance of the variant calling pipeline by comparing variant calls from a sample within the project to known “gold standard” variant data that already exist for that sample.  This “gold standard” data can encompass variants identified with high confidence by other experimental or computational approaches. 

Task Dialog

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 and Benchmark target regions, the former relating to the regions sequenced in this study and the later the regions that have been sequenced and contain the “gold standard” variant calls.  This parameter is important to ensure that only overlapping regions are compared, avoiding the identification of false positives or false negative variants in regions covered by only project sample or the “gold standard” sample.  The Validated variants file is a vcf file containing the “gold standard” variant calls for the sample of interest, and can be previously associated with Partek^® Flow^® as a Variant Annotation Database via Library File Management or added on the fly.

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