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Old 02-11-2013, 01:46 PM   #2
Bukowski
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Location: Aberdeen, Scotland

Join Date: Jan 2010
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Yes. If you have PCR or optical duplicates you will want to remove them before variant calling or you may introduce spurious variant calls.

It does depend what method you have used to do the capture, some methods are not amenable to deduplication - amplicon based approaches etc. A straightforward in-solution capture approach will be fine because you've randomly sheared your DNA before capture, and therefore you shouldn't expect lots of read pairs with the same coordinates when mapped.
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