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Old 03-31-2016, 09:33 AM   #2
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 700
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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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