Please make an issue request on the Picard github page. Unfortunately I
cannot say when our team will be able implement such a feature. Sincerely,
Nils Homer
On Thu, Sep 18, 2014 at 4:20 AM, Kanterakis, Efstathios <
[email protected]> wrote:
> Hi Nils,
>
> Thank you for your response. Unfortunately my java skills are quite rusty.
>
> Could I ask this as a feature request for a future release?
>
> Thank you.
>
> Stathis
>
>
>
>
>
> *From:* Nils Homer [mailto:[email protected]]
> *Sent:* 16 September 2014 09:33
> *To:* Kanterakis, Efstathios
> *Cc:* [email protected]
> *Subject:* Re: [Samtools-help] CollectTargetedPcrMetrics concatenates
> overlapping intervals
>
>
>
> 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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