My suggestion would be sanitize the read names,
N
On Fri, Oct 17, 2014 at 3:04 PM, Richard Corbett <rcorb...@bcgsc.ca> wrote:
> Hi all,
>
> Our usual read name format in a bam is something like:
> HS13_248:4:2111:2846:54933
>
> But we just were asked to analyse some data where the read names in the
> bam have this format:
> HWI-ST909_0086:3:1101:19761:56275#CGATGT/2/
>
> I notice that while running MarkDuplicates in version 1.122, the live
> messages suggest that Picard can't identify the pairs because of the
> terminal /1/ and /2/ in the read names:
> ...
> INFO 2014-10-17 11:55:18 MarkDuplicates Read 114,000,000
> records. Elapsed time: 00:21:07s. Time for last 1,000,000: 12s. Last
> read position: GL000212.1:39,902
> INFO 2014-10-17 11:55:18 MarkDuplicates Tracking 112566758 as
> yet unmatched pairs. 2570 records in RAM.
> ...
>
> However, at the end of the run, there are still some reads properly
> marked as duplicates.
>
> Is it ok to ignore the warnings about unmatched pairs, or should we go
> back and edit the read names in the fastqs to ensure our duplicate marking
> ?
>
> thanks for all your help,
> RIchard
>
>
>
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