You can visualize it.
Often visualization of a region around a snp can give a good clue as to what's going on.
Some are "slam dunks", others are "well .. maybe" and others are "nope".
I suspect that attempts to make 99% accurate calling is frustrated by several things: repeats, homo-polymer runs, inaccurate reference, near duplicate regions, chemistry problems, etc. It takes a bit of practice, but a quick, but knowledgeable eye can spot some problems.
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