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Old 06-21-2016, 12:51 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

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I assume you are talking about exome-capture?

There is no important difference between on- and off-target reads. Variants outside target regions may be of interest, though it's less likely; and of course 99.99% of variants inside the target are of no interest, but presumably they will tend to be more interesting than the ones outside the targets. Note that the gene annotations are continuously evolving as new genes and isoforms are discovered, while baits for capture kits may be based on annotation from many years earlier.

If the capture was successful, then yes, the coverage will be much higher within the targets than outside.
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