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:nho...@broadinstitute.org]
Sent: 16 September 2014 09:33
To: Kanterakis, Efstathios
Cc: samtools-help@lists.sourceforge.net
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
<ekantera...@illumina.com<mailto:ekantera...@illumina.com>> 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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