Patient tab, Samples sub-tab

Geneticist Assistant Online Help : Managing Patients and Runs : Accessing and Reviewing Patient Records : To review existing patient information on the Patient tab : Patient tab, Samples sub-tab

The Samples sub-tab on the Patient tab has a single pane, the Samples pane, that displays all the samples that are associated with the patient as well as information about the samples.

You can do the following on the Samples sub-tab:

• View the details for an individual patient sample.

• View the sample variants filtered by a selected panel.

• View the coverage information for all regions in a sample panel.

• Calculate the panel statistics for a patient sample.

• Set sample permissions.

• View the patient samples in a third-party viewer (NextGENe or IGV).

• Export the patient samples to a VCF file.

• Generate Sample reports for one or more selected samples.

• Generate a Batch Variants report for a selected sample or samples.

• Generate a Batch Coverage report for a selected sample or samples.

You can right-click a sample in the Samples pane to open a context menu with the following options for working with the sample:


Option	Description
Sample Details	Opens the Sample tab, which contains detailed information about the associated sample, including the variant list. See Geneticist Assistant Data Review - Sample Tab. Note: You can also double-click the sample to open the Sample tab.
Show Sample Variants Filtered by Panel	Opens the Select Panel to Filter Variants dialog box. Select a panel in the dialog box to show the variants in the patient’s sample filtered by the selected panel or panels.
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 the sample. See Reviewing Panel Statistics.
Copy	Copies all the information that is displayed for the selected associated sample to your client’s clipboard. You can then use standard Paste commands to paste this copied information into a third-party application such as Notepad.
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 the patient sample. See Setting Read and Write Permissions.
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. Note: For more information about standard reports, see Geneticist Assistant Reports.
Create Batch Variants Report	Generates the Batch Variants report for the selected 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 sample or samples. (CTRL-click to select multiple samples.) See Generating a Batch Coverage Report.
Load Columns
Manually	Opens the Select Columns dialog box in which you can select columns that are to be shown and clear the columns that are to be hidden dynamically, or select a configuration from the list of available column configurations. This option is also available on the column header context menu for the sub-tab. Note: For information about showing and hiding columns dynamically, see To show/hide columns in a tab pane. Note: If you set column display preferences here, then you can display preferences for variants in all the variant sub-tabs and panes (with the exception of the Sample Group columns on the Sample Variant Data sub-tab on the Sample tab and the Variant pane on the Variant tab) in a single step. See To apply shared preferences or to clear all tab preferences.
Compact	Displays the data columns on the sub-tab in a more condensed view. To toggle the display, click Compact as needed.
<Saved Pane Configuration Name> - Saved by <User Name>	Publicly available pane configurations. The name of the user who created a pane configuration is displayed next to the configuration name.
Load Filters
Manually	Opens the Filters table for the Samples pane. See To filter the data that is displayed in a tab pane.
<Filter Template Name> - Saved by <User Name>	Opens the saved Filter template for the Samples pane. Limits the display in the pane to only the data (fields) that are defined by the template. See To filter the data that is displayed in a tab pane.