Variants

Charlene Son-Rigby -

The Variants table is used in Clinical Reporter in the Variant Interpretation and Variant Selection pages and in Variant Miner to display all variants in a test or report. The table provides a variety of information about each variant that varies based on the module in which the table is used and the test or report type. To the left of the table is the Filters menu with filtering options corresponding to the displayed information in the table. 

Navigation

The Variants table is used in the following pages:
- Clinical Reporter  >>  Actions menu  >>  Interpret Variants option
- Clinical Reporter >>  Actions menu  >>  Review Variants option
- Clinical Reporter >>  Actions menu  >>  View Interpretation option

- Projects list view >>  Report Type link

Features

Each row in the Variants table represents one variation, meaning one variant allele for a position. If more than one alternate allele was called for a position each allele is represented in a separate row.

Variant Types

VCF files can contain both small variants such as SNVs and InDels, and Structural Variants. To optimally represent variants in Opal the different variant types are displayed under separate tabs within the Variants table. Click on the tab at the top of the table to switch from viewing SNVs and InDels to viewing Structural VariantsNote that both Structural Variant data and CNV data (including copy number) are displayed under the Structural Variants tab.

The following articles, SNVs and InDels and Structural Variants, describe all possible columns in the Variants table as well as the options in the corresponding Filters menu for each the variant types.

The detailed information on each variant specific to the Variant Interpretation in Clinical Reporter, such as the variant scoring details and classification history, are described in the Variant Detail article. 

 

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