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. 

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 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^® as a Variant Annotation Database via Library File Management or added on the fly.

The Validate variants results page contains statistics related to the comparison of variants in the project sample compared to the validated variant calls for the sample (Figure 2).  The results are split in to two sections, one based on metrics calculated from the comparison of SNVs and the other from the comparison of INDELs.  

The following SNP-level metrics are contained within the report, comparing the sample in the project to the validated variant data:

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The INDEL-level metrics columns contained within the report are identical, with the expeption of a lack of information with regards to transitions and transversion.

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