Unfortunately there is not an option currently to not merge overlapping
intervals. We would be able to accept a patch if you have the time to add
this improvement. Your other alternative for a quick and dirty solution is
to run it multiple times, each time with non-overlapping intervals.
Nils
O
Hello,
I've noticed that Picard's CollectTargetedPcrMetrics will concatenate
overlapping intervals in the PER_TARGET_COVERAGE output. For example:
chr3 93692457 93692581 + 1_PROS1_4
chr3 93692546 93692664 + 1_PROS1
