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the order of merge and mark duplicate
I have a whole genome sequencing sample.
That consist of 1fastq file per lane.
That consist of multiple file per sample that produced per lane.
After I merge multiple bams, I progress MarkDuplicates using Picard.
But MarkDuplicates is very slow.
So I want to progress MarkDupllicate using bam per lane, then merge bam files.
I wonder whether the order of merge and MarkDuplicate affect post-analysis?