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Remove duplicates from Targetted sequencing using amplicon approach?
I am performing variant calling on Targetted exome samples using GATK (V2014.3-3.2.2-7-g f9cba99)
My samples are amplicon based targetted sequences.
I observe that Picard MarkDuplicate step marked more than 85 percent of the reads as duplicates. My question is :
1) Is it natural that targettted deep sequencing generates samples with high percent of duplicate reads? (Due to the fact that a small region if resequenced to obtain 300 X coverage, is expected to produce a large number of duplicated reads)
2) Is it OK to omit the MarkDuplicate step and proceed with variant calling steps considering the duplicates as well.