To set the reference region settings for an mtDNA project
1. Do one of the following:
• If the Filter Settings dialog box is already open, then open the Mito Alignment tab. Go to Step 2.
• On the Mito Alignment viewer main menu, click Filter Settings.
The Filter Settings dialog box opens. The Mito Alignment tab is the open tab.
2. Do one of the following:
• Review the default settings, and if you are satisfied that the Mito Alignment filter settings are appropriate as-is for your project, then go to Step 3.
• Edit any of the default values for the Mito Alignment filter settings. See the table below.
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 | If you edit any of the default values for the Mito Variant filter settings, you can click Default, and then click Yes in the Default values message that opens and all values are immediately reset to their default values. |
• Click Load to open the Load Filter Settings dialog box, and then browse to and select a Filter Settings (.settings) file.
Both Mito tabs are populated with the values in the settings file. You can leave the values as-is on the Mito Alignment tab, or you can edit any of the values before you apply the settings. See the table below.
Option | Description |
|---|---|
Template Length | Optional. Select to filter reads for paired data. The paired read is kept if the read length is > (TLEN) or < - (TLEN). You can leave the default value set to 100, or you can edit the value. Note: If the data is non-paired, then read length is used for filtering. |
Variant Calling (You must select one option.) | |
• Entire Reference: The default value. Select to call variants in any region. | |
• Input Region: Select to call variants in a single specific region. If you select this option, then you must adjust the Start and End values. | |
• Input Region: Select to call variants in multiple specific regions. If you select this option, then you can manually adjust the Start and End values for each region, or you can select Load BED File, and then in the Load BED Settings dialog box that opens, browse to and select the BED file that defines these multiple regions. Note: For detailed information about the format for a BED file, see BED file. After you load a BED file, you can use the Add option and the Remove or Remove All options to add and remove regions for the file. If you add a region, you must specify the Start and End positions for it. Positions in a BED file are inclusive, start through end. | |
3. Do one of the following:
• Click OK to close the Filter Settings dialog box and immediately update the Mito Alignment viewer display based on the applied settings.
• If you edited any of the filter settings and want to save these edits before applying them, then click Save to open the Save Filter Settings dialog box and save the filter settings to a Filter Settings (.settings) file.
Note the following about saving a Filter Settings file:
• You must enter a name for the file.
• The file type is Filter Settings File (.settings) and you cannot change this.
• The default location for saving the Filter Settings file is the project folder, but you can always select a different location.
• You cannot save individual filter settings files for the Mito Variant tab and the Mito Alignment tab. All settings on both Mito tabs are saved when you save a filter settings file for an mtDNA project.
After you save the filter settings file, you can click OK to close the Filter Settings dialog box and immediately update the Mito Alignment viewer display based on the applied settings.