Cases Tab

A case is an analysis result in VCF or gVCF file format that has been imported and annotated. The Cases tab lists all cases for your account or workgroup.

BaseSpace Variant Interpreter creates a case for each imported analysis result, and populates the case with the variants called for the sample. Enter subject and sample metadata for each case individually, or add metadata for multiple cases using a sample metadata manifest.

From the Cases tab, you can import analysis results and begin working with a case.

The following columns provide an overview of each case:

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Analysis Result—Lists the name of the case. The default name is the VCF file name. Select to open the case.

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Subject ID—Lists the unique ID for the subject. Select the subject ID to view details.

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Sample—Lists the unique ID for the analysis result.

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Project—Lists the project that contains the analysis result.

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Genome Build—The reference genome assembly used for annotation.

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Status—Indicates the status of the case or analysis file: Processing, Failed, Completed, Inactive, Action Required, Pending Review, In Progress, Awaiting Approval, or Closed. Select a status entry to update the case status and owner.

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Owner—The owner assigned to the case.

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Data Type—Indicates the type of analysis.

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Tumor-Only—A tumor workflow produced the analysis result. If defined, data type includes the type of tumor.

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Tumor-Normal—A tumor workflow using paired and normal samples produced the analysis result. If defined, data type includes the type of tumor.

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Germline—A germline workflow produced the analysis result.

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Unknown—The type of sample is unknown, likely because the data could not be extracted from the file.

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Type of Variants—Indicates the type of variants in the analysis result.

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Created Date/Last Updated Date—Lists the dates the analysis file was imported or last updated. The column sort order uses last updated date.

The unnamed final column contains file details. Select the column to view the file details, which include the result path that links to the case in a sample metadata manifest. A result path is generated for every imported VCF.

If metadata exceeds the column width, expand the column or hover over text.