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PCR Duplicate detection on PCR-Free Libraries
We've just started a big project in which we plan to use GATK with PCR-Free Libraries & I was curious as to what your thoughts are on using PCR Duplicate detection (MarkDuplicates) with the currently Illumina PCR-Free libraries? Internally do you still run this stage of the GATK pipeline with the new libraries?
Looking at your best practices documents I see it's still in there, but didn't see anything mentioning PCR-Free libraries.