Transparency can switch off any color from the original image on the final map. This option is typically used to eliminate borders of multiple map sheets that are stitched together. You can set a specific color of the map to be considered fully transparent during rendering.
It is available in Advanced image settings which can be accessed from the screen which is available prior to the rendering by clicking on the Advanced options button.
If you set the Ignore alpha channel (4th band) check button on, the alpha channel from input images will be ignored.
Picking own color for transparency
In the Transparency settings switch to Color to Alpha option.
Define a color manually
Now click on the color preview or Change button and you will get standard color picking options where you can define color by HEX value, Hue + Saturation + Value, setting RGB values, picking from a few color palettes or by using a picking tool which allows you to click anywhere on your computer.
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Pick a color from your image
If you want to select the color for transparency from the image you are processing, click on the Pick a color button.
It will open a new window with your image, where you pick any color from the picture.
The picked color will show up in a pop-up with RGB + HEX values and in the top right corner in HEX format.
Now confirm your selection by clicking on the Select color button.
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For transparency settings in command-line, see the MapTiler manual.