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Depth of Coverage using overlapping windows

lkeelerlkeeler CaliforniaMember

Hi GATK team,
I am currently using the Depth of Coverage option for GATK for a precursor to detect CNVs. I had to specify intervals that did not overlap in order to get individual predictions for the depth of coverage for each interval by skipping a base between intervals, because if I did not, it would merge the intervals into larger than desired fragments. Is there a way to stop GATK from merging the intervals if they overlap? I would love to get coverage in a sliding widow approach instead.

Thanks!
Lauryn

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