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We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
Depth of Coverage using overlapping windows
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.