@mikeshilov,
In case of Box & Whisker chart, you can customize the thickness of both whisker & stem by using whiskerThickness & stemThickness properties respectively.
If you are still unable to fulfill your requirements, kindly create JSFiddle with your use-case and share it with us so that we can look into the code, run it to understand the scenario better and help you achieve your requirements.
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Indranil Deo,
Team CanvasJS