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Referring to broadinstitute.org/gatk/guide/article?id=3060, is removing duplicates necessary to be done twice, once per-lane and then per-sample?
Is it not enough to just mark the duplicates in the final BAM file with all the lanes merged, which should remove both optical and PCR duplicates (I am using Picard MarkDuplicates.jar)? So specifically, in the link above what is wrong with generating -
Then, merging them to get
and finally, include "de-dupping" only for the merged BAM file.