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In the event paired samples exist within the project, detection Among samples can be utilized to identify loci with differing genotypes between the pair once each sample has been compared to the reference sequence assembly.   To  In instances where there is limited information to accurately determine genotypes in one or both of the samples, the same genotype may be called for case and control if it differs from the reference.  The Filter variants task can be used to exclude these spurious loci.  To perform this analysis, sample attributes must be added in the Data tab of the project (Figure 2).  Specifically, an attribute must be added for sample ID (shared between the paired samples) and an attribute must also be added for sample type that differentiates the paired samples.  Examples of the latter can include case and control or tumor and normal.  If these attributes are present, a section for Analysis options will be displayed below the Variant detection method (Figure 3).  To utilize this feature, select Paired analysis.  Match ID must then be specified and should correspond to the attribute that references the sample ID shared between the pair.   Selecting Case/control will allow for discriminating genotypes between paired samples in downstream tasks.  Attribute should correspond to the attribute that defines type within sample pairs, and Control can be specified for whatever category relates to the reference sample.

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