I am trying to analyze data that sequenced targeted regions of the genome (about 500 Mb in total). In the GATK pipeline it suggests marking duplicates/removing duplicates. Is this important to do with targeted sequencing? Wouldn't you expect duplicates because of the experimental design? Thanks!
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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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