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GATK4 CollectHsMetrics - How to avoid the overlap of adjacent intervals ?
I'm trying to access the quality of my targeted experiment, and I'm interested on saving the per target information using the --PER_TARGET_COVERAGE argument. However, I observed that when coordinates of the intervals are adjacent, they are merged in the output:
I want to analyse each target separately, so I tried to add --interval_merging=OVERLAPPING_ONLY option but the argument isn't recognized by the tool:
interval_merging is not a recognized option
How can I avoid this behavior?
Thanks in advance,