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
On Tue, Sep 16, 2014 at 1:41 PM, Kanterakis, Efstathios <
[email protected]> wrote:
> 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_5
>
>
>
> becomes:
>
> chr3 93692457 93692664 208
> 1_PROS1_4|1_PROS1_5
>
>
>
> Is there a way of switching this behavior off? The reason being that I’m
> trying to collate other statistics to that file and this causes the rows
> not to match.
>
>
>
> Thank you,
>
> Stathis
>
>
>
>
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