To add a run
1. On the Geneticist Assistant main menu, click File > New Run.
The New Run dialog box opens.
2. Enter the name for the new run.
 | The name can have a maximum of 255 characters. Spaces are allowed. |
3. Specify the run settings.
Setting | Description |
|---|---|
Required Settings | |
Chemistry | If the correct chemistry is not available, then you can add it. Click New to open the Add New Chemistry dialog box and add the new chemistry. |
Instrument | If the correct instrument is not available, then you can add it. Click New to open the Add New Instrument dialog box and add the new instrument. |
Reference | If the correct references are not available, then you might need to specify the reference directory and/or add the necessary references to the directory. For information about specifying the reference directory, see Specifying your Geneticist Assistant Settings. For information about downloading the most recent references, see Updating References. Note: This is a run-specific option. You also have the option of setting this option on a per sample basis later in the process. |
Panel | After you select a panel, the panel group is automatically selected and the name is displayed in the Panel Group field. Note: If the correct panel is not available, then you can add it. Click New to open the Manage Panels dialog box and import the needed panel. See Importing a Panel. Note: This is a run-specific option. You also have the option of setting this option on a per sample basis later in the process. |
Panel Group | Read-only field that displays the name of the group to which the selected panel belongs. |
Quality Metric Profile | If the correct quality metric profile is not available, then you can add it. Click New to open the Manage Quality Metrics dialog box and add the profile. See Managing Quality Metrics. |
Owner | By default, Owner is set to your user name. Optionally, you can select a different owner for the run. If the appropriate user is not available, and you are an Administrator user or a user with the correct permissions, then you can add the new user. Click New to open the Add New User dialog box and add the new user. See Managing Users. |
Multiple Samples in VCF | Select this option if you are loading a VCF file that contains variants from multiple samples. |
Optional Settings | |
Run Date/Time | The default value for the Run Date and Time is the current day’s date and time, but you can change one or both values as needed. To change a value, select the value, for example, the month, and then you can manually enter the new value, or you can use the Up/Down field arrows to change the value. Note: You must select each value that you are changing one at a time. If you set the Run Date/Time here, then this is a run-specific option. You also have the option of setting this option on a per sample basis later in the process. |
User Group | By default, non-administrative users have read/write access to only those runs that they submitted. If other non-administrator users are to have read/write access to this run, then select the appropriate user group. |
Sample Group | Optional. Used for a group of samples that are to be processed repeatedly over a period of time, for example, a group of control samples for which the coverage or variant frequency is to be tracked. If the correct Sample Group is not available, then you can add it. Click New to open the Add New Sample Group dialog box and add the new sample group. Note: This is a run-specific option. You also have the option of setting this option on a per sample basis later in the process. |
Subpanel | To verify coverage for a smaller number of regions that are within the panel that has been selected for the run, select the appropriate subpanel. Note: If no subpanels have been created for the selected panel, then no options are available on the Subpanel dropdown list. For information about creating subpanels, see Adding a Subpanel. |
Submit Coverage | Selected by default. If BAM files are included in the run, then select this option to import coverage information for the panel regions from the BAM files. Clear this option to skip the coverage import. |
Import from VCF | Selected by default. If you are loading a VCF file that contains pathogenicity information (pathogenicity and status) and variant comments, then by default, this information is imported into the Geneticist Assistant database. • Pathogenicity and status - Selected by default. Note: This is a run-specific option. You also have the option of setting this option on a per sample basis later in the process. • Comment - Selected by default. • Artifact type - Select to submit any artifact any information that the loaded VCF file contains. |
Submit Hotspots | If any variants in the loaded VCF file have an allele frequency value = 0, then select this option to submit these variants to the Geneticist Assistant database. |
Accepted VCF filters | Applicable after you load sample files. See Step 5. |
Identify Patient ID | |
Add New Patient | If the correct patient is not available to associate with a sample for a run, then you can click this option to open the Add New Patient dialog box and add the patient. See Step 6. |
• from Sample Name | • Automatically match a patient ID based on the sample file name and the selected separator. For example, if the separator is a period, then all text up to the first period in the sample file name is used as the patient ID. |
• from File | • Match the sample with the patient ID as defined in the provided tab-separated values file, with 1 patient/sample per line in the file containing two fields: sample name followed by a tab, and then patient ID. |
Split Sample Name by Separator | Selected by default. If you clear this option, then the entire VCF sample file name is used as the patient ID. Select the separator that you are using to define the patient ID from the sample file name. |
4. Do one of the following:
• To automatically load all the applicable sample files (VCF only or VCF and BAM files) that are in the same folder in a single step, do the following:
• Click Select Directory to open the Select Directory dialog box,
• In the Select Directory dialog box, browse to and select the appropriate directory, and then click Select Folder.
• To manually select sample files, do the following:
• Click Select Variant and/or Coverage Files to open the Select Files dialog box.
• In the Select Files dialog box, browse to and select the BAM coverage file and/or variant (VCF) files that are to be loaded, and then click Open.
When selecting the files that are to be loaded, note the following:
• You can load a VCF or BAM file for a new run that has been submitted previously for another run. You can keep the sample name the same, or you can edit the sample name as needed.
• You can use the same run name to load additional sample files (BAM and/or VCF) for a previously submitted run. The additional sample files are processed and appended to the run.
• At a minimum, you must always load a VCF file. Optionally, you can also load a BAM file to include coverage information for the panel regions.
• If you have a single sample to load, and the VCF and BAM file names do not contain corresponding fields in the file names, then select the VCF or BAM file, and then after you click Open, the file is placed in the appropriate field for the sample entry. You can then click the Browse button 
next to the appropriate file type to load the corresponding file for the sample. For example, if you loaded a BAM file, then you can click the Browse button next to the Variant File (*.vcf) field for the sample entry to load the needed VCF file for the sample.
next to the appropriate file type to load the corresponding file for the sample. For example, if you loaded a BAM file, then you can click the Browse button next to the Variant File (*.vcf) field for the sample entry to load the needed VCF file for the sample.• If you have multiple samples to load and the VCF and BAM files do not contain corresponding fields in the file names, then CTRL-click as you select only the VCF files or the BAM files, and then after you click Open, each file is placed in its own sample entry. For each sample entry, you can then click the Browse button next to the appropriate file type to load the corresponding file. For example, if you loaded a BAM file, then you can click the Browse button next to the Variant File (*.vcf) field for the sample entry to load the needed VCF file for the sample.
next to the appropriate file type to load the corresponding file. For example, if you loaded a BAM file, then you can click the Browse button next to the Variant File (*.vcf) field for the sample entry to load the needed VCF file for the sample.• If you are loading both a VCF file and a BAM file, and the files do contain corresponding fields in the file names, then CTRL-click as you select both the VCF and BAM files, and then after you click Open, both files are loaded into the appropriate fields for the same sample entry in a single step. You can load a single VCF/BAM file combination this way, or you can load multiple VCF/BAM file combinations. Each correspondingly named VCF/BAM file combination is placed in its own sample entry.
• If you have multiple BAM files for a sample, you do not need to submit each file as an individual sample, and then assign each file to the same patient. Instead, you can use the Merge BAM Files tool to merge all the BAM files into one file and then submit the file as a single sample. See Merging BAM Files with the Merge BAM Files Tool.
• By default, the sample name is set to the VCF file name. The name is displayed at the top of the sample entry. You can edit the sample name.
• If you load a sample file in error, then you can right-click anywhere in the sample entry area, and then click Remove this sample.
After the files are loaded for a sample, the full directory paths (directory and file name) for the loaded files are displayed in the appropriate fields for each sample entry at the bottom of the New Run dialog box.
 | After you load sample files from a specific directory, if BAM files are included, then the BAM files must remain in this directory. You cannot move these BAM files to a different directory after you have successfully submitted the files for a run. |
5. After you load your sample VCF files, do one of the following:
• To import only those sample variants that have been flagged as passing (Pass) the filter values in the loaded VCF files into your Geneticist Assistant database, leave Accepted VCF filters set to the default value of Pass.
• To set additional filter types to be imported from the VCF, click Edit to open the Select Accepted Filters dialog box, and then select the values from the list of available filters. The options that are available depend on the filter values that are included in the loaded VCF files.
| | This is a run-specific option. You also have the option of setting this option on a per sample basis later in the process. |
After you select the filters, and then click OK, the Select Accepted Filters dialog box closes. The selected filters replace the default value of All.
6. Optionally, for each sample, do any or all of the following:
• Edit the sample name.
| | You can click Default at any time to return the sample name to its default value. |
• By default, the Reference, Panel, Run Date/Time, Sample Group, and Import Pathogenicity from VCF values that are indicated for a sample are the run-specific values that you specified in Step 3. You can edit any or all these values on a per sample basis.
| | If you edit the panel on per sample basis, then the panel group might also be modified, but you cannot edit the panel group directly. |
• To associate a patient with a sample, select a patient on the Patients dropdown list.
| | If the correct patient is not available, then you can click Add New Patient to add the patient. See Adding Patients. |
• By default, if you have specified variant filters, then these filters are applied at the run level. To edit the accepted variant filters for a sample, click Edit, and then in the Select Accepted Filters dialog box, edit the filter selection.
7. Click OK.
The Current Jobs tab opens and a progress bar that shows the progress of loading the files is displayed on the Current Jobs tab. After the files are successfully loaded, the progress bar is removed from the Current Jobs tab. You return to the Runs tab. The new run is displayed on the Runs tab. You can now review the data for the run. See Geneticist Assistant Data Review - Runs Tab.