Geneticist Assistant Online Help : Geneticist Assistant Setup and Maintenance : Managing Quality Metrics : To add a new metric profile
To add a new metric profile
1. On the Geneticist Assistant main menu, click File > Manage Quality Metrics.
The Manage Quality Metrics dialog box opens.
2. Click New.
The New Metric Profile dialog box opens.
3. Enter a name for the new metric profile, and then click OK.
The New Metric Profile dialog box closes and the Manage Quality Metrics dialog box remains open. The name of the new profile is displayed in the Edit profile field, and the lower (Metrics) pane is blank.
4. The Used for field identifies the samples types for which the metric profile should be used. When you are creating a new metric profile, the default value is the value for the last loaded metric profile. You can leave this value as-is, or optionally, in the Used for field, enter the sample type for which the profile applies, and then click the Confirm icon that is displayed to the right of the Used for field.
 
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As you enter a value in the Used for field, a Reset icon is displayed to the right of the Confirm icon. If you decide that you would rather use the value that had previously been displayed in the field instead of your new value, click the Reset icon.
 
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You must repeat Step 5 through Step 9 for each quality metric that you are adding to the metric profile.
5. In the Select or type new metric field, open the dropdown list and select a pre-loaded metric, or manually enter a metric name. If you manually enter the metric name, you can enter the name for a pre-loaded metric, or you can enter a user-defined metric (one that is not available on the pre-loaded metric list), for example, NextGENe Score. Note the following if you enter the name for a pre-loaded metric:
• As you enter the metric name, a dropdown list opens. The list is dynamically updated with the names of the pre-loaded metrics that match the search string that you are entering.
• The search string is not case-sensitive, and the string can be found anywhere in the metric name. For example, a search string of “alle” returns Allele fraction, % of bases called that are variants, and so on.
6. Click Add.
• If the metric is a metric that is commonly defined in a VCF file, then the metric with its attributes (Category, Use, and Data Type) and default threshold placeholders is added to the profile and displayed in the lower (Metric) pane of the Manage Quality Metrics dialog box. The Data Source field displays the location in the sample VCF file where the metric is found. Go to Step 8.
• If the metric is a user-defined metric, then you must select the Category, Use, and Data Type values for the metric. You select these values from a list of pre-defined values and you cannot add a new value, or edit the available values. The Use is always set to a default value of REQ (required), but you can select OPT (optional), or OHR (Optiona1but Highly Recommended). The Data Source field is blank. Go to Step 7.
 
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If you are having difficulty locating your user-defined metric in the metric list, remember, you can click a column header to sort the display. See To change the sort order of data.
 
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To remove a metric from the profile, right-click the metric, and on the context menu that opens, click Remove Metric.
7. Double-click in the Data Sources field to open the Edit Data Source dialog box, and then browse to and select the appropriate template file and define the data source.
8. Set the metric thresholds. To set a threshold, make sure that the checkbox for the threshold is selected, and then double-click the threshold placeholder to select it and then change the value.
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You can always set a Minimum threshold value, a Maximum threshold value, and/or Warning threshold values for a metric; however, not all thresholds are applicable for all metrics.
9. If applicable, define the calculation for the metric.
10. Optionally, to save the metric profile in .json format, click Save as json, and then specify a name for the quality metric profile and the location in which to save it.
 
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This option is useful for sharing your metric profiles with other users. You can send this file to Geneticist Assistant users, and they can use the From json function to import the file and use the profile in their Geneticist Assistant instances.
11. Click OK.
The Manage Quality Metrics dialog box closes and the profile is saved to your Geneticist Assistant database. The profile is now available for selection when adding a new run.