To edit the Comparison viewer variant highlighting colors
The Comparison viewer is divided into two panes: the Sample to Sample Comparison (top) pane and the Variant Comparison (bottom) pane.
• You can specify the variant highlighting colors in the Sample to Sample Comparison pane, where the default colors are the following:
• Diagonal cells that compare a sample to itself are highlighted in black.
• All other cells in the correlation table compare one sample to another and are highlighted in a blue color gradient from 0 to 100%, where 0% cells are blank/white.
• You can specify the variant highlighting colors in the Variant Comparison pane, where the default colors are the following:
• Variants that can be classified as a major allele are highlighted in blue.
• Variants that can be classified as a minor allele are highlighted in gold.
• If a variant was determined to be a Low Coverage variant, the variant is highlighted in red.
1. On the Application Settings dialog box, ensure that the correct sub-pane, Comparison viewer: Sample to Sample or Comparison viewer: Variant, is visible.
2. Double-click the color swatch that is displayed for a variant highlighting color to open the Select Color dialog box, select a different color, and then click OK.
The Select Color dialog box closes and the Application Settings dialog box remains open. The newly selected color is displayed for the selected sample or variant type.
3. Do one of the following:
• If you are done specifying your settings, then click Save to close the Application Settings dialog box and return to the GeneMarkerHTS main window.
• Continue to edit other application settings as needed.