Your Variant Caller Tells You How Confident It Is. Have You Ever Checked If It's Telling the Truth?

Every variant caller you have ever used attaches a number to each call: QUAL. It is a confidence score, a claim about how likely the call is to be correct. You filter on it constantly. QUAL >= 30, QUAL >= 20, whatever your pipeline settled on years ago. Here is a question almost nobody asks: is that