Re: [Samtools-help] dup behaviour for samtools vs picard

[Nava W. <ne...@sg...>]

hmm, might be neat to have a samtools validate tool which checks if a
sam file conforms to the spec.

On Thu, Aug 06, 2009 at 09:14:15AM -0400, Tim Fennell wrote:
> I'd expect that what's happening is probably a result of violating one  
> or more constraints in the sam spec.  For example, I'm not entirely  
> sure how things would be affected if there are four reads/records in  
> the file with the same name as would happen if you merge a file with  
> itself.
> 
> -t
> 
> On Aug 6, 2009, at 6:53 AM, Sendu Bala wrote:
> 
> > When you do something silly like merge a bam with itself, why  
> > doesn't an
> > rmdup/MarkDuplicates see the duplicate reads as duplicates? And why do
> > samtools and picard behave so differently in this case?
> >
> > For example, starting with a 2000 read bam file that both samtools and
> > picard agree has 6 duplicate reads, merged with itself it becomes 4000
> > reads. Then on the merged bam:
> >
> > picard-tools MarkDuplicates marks 28 reads as duplicates.
> >
> > samtools rmdup gets rid of 1073 reads.
> >
> > I'd have naively expected 2006 reads to be seen as duplicates. Or
> > perhaps 12. Or even 6 again. But those results just seem random?
> >
> >
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