Sample Detail

Opens the Sample tab for the sample. See Geneticist Assistant Data Review - Sample Tab.

Show Samples Filtered by Panel

Displays all the variants in the selected samples filtered by a selected panel or panels. If you select this option, then the Select Panel to Filter Variants dialog box opens. You must select a panel or panels in this dialog box by which to filter the variants for the selected samples.

Coverage Regions

Opens the Coverage Regions tab, which lists the coverage information for every region in the panel for the associated sample. See Coverage Regions tab.

Panel Statistics

Opens the Panel Statistics tab. The tab has options for displaying specific information based on the panel that was used for a sample’s run. See Reviewing Panel Statistics.

Permissions

Opens the Permissions dialog box.You use the options on this dialog box to set or edit the permissions (Can Read or Can Read and Can Write) that the specified users or groups are to have for selected samples. See Setting Read and Write Permissions.

Change Ownership

Opens the Change Sample Ownership dialog box, which displays the name of the current owner for the selected sample, and an option (New Owner) for selecting a new owner for the sample. You can change the ownership for any sample if you are an Administrator user, the current owner of the sample, or if you have been granted Can Read and Can Write permissions for the sample.

External - Contains all the sub-menu options for viewing the sample variants in a tool that is outside Geneticist Assistant.

View in NextGENe

Requires you to have your NextGENe installation specified in your Geneticist Assistant settings. (See To configure Geneticist Assistant directories.) If selected, then Geneticist Assistant browses for the folder where the VCF file for the sample is located. If the NextGENe project file is found in the same directory as the VCF file, then the NextGENe project is opened in the NextGENe Viewer.

View in IGV

Applicable if there is a corresponding BAM file (and not a NextGENe project file) in the same folder as the VCF file for the sample. Opens the BAM file in the third-party Integrative Genomics Viewer (IGV).

Export - Contains all the sub-menu options for exporting a variant.

Export to VCF

Exports all the variants in the selected sample or samples (CTRL-click to select multiple samples) to a VCF file. You must specify both the file name and the location in which to save the file.

Save Sample Reports

Applicable for one or more samples. CTRL-click to select multiple samples. Generates an individual sample report for each selected sample. If a single sample is selected, then a default location, report name, and report type (.csv) are provided, but you can change any or all of these values. If multiple samples are selected, then you can select only the location in which to save the report. Each report is named the same as the sample and the report format is .csv, and you cannot change either of these values.

Create Batch Variants Report

Generates the Batch Variants report for the selected associated sample or samples. (CTRL-click to select multiple samples.) See Managing a Batch Variants Report.

Create Batch Coverage Report

Generates the Batch Coverage report for the selected associated sample or samples. (CTRL-click to select multiple samples.) See Generating a Batch Coverage Report.