[miso-users] MISO Handling of Marked Duplicates

[Fong Chun Chan]

Hi Yarden,

Thanks for the reply.

Just to clarify, I was referring to PCR duplicates and therefore the
duplicates marked will NOT have the same read ID but simply have a flag in
the *.bam file indicating it is a PCR duplicate. So If I understand you
correctly, if I were to pass in my GSNAP bam with duplicates marked using
PICARD tools then currently MISO will just treat each of the duplicates
independently?

Fong


On Mon, Nov 19, 2012 at 3:10 PM, Yarden Katz <yarden at mit.edu> wrote:

> Hi Fong,
>
> There's no explicit handling of duplicates, but that can be added.  In
> general, if you have paired-end reads, they will be paired by the read ID,
> in which case duplicates that have the same ID will not be treated
> separately.  For single-end reads, duplicates with distinct IDs will be
> treated as independent reads, and a SAM flag marking duplicates will be
> ignored.  Please let me know if you have any questions about this.
>
> Best, --Yarden
>
>
>
> On Nov 19, 2012, at 4:57 PM, Fong Chun Chan wrote:
>
> > Hi,
> >
> > I have some GSNAP aligned bam files that have been post-processed with
> GATK to mark duplicates. How does MISO handle *.bam files that have been
> duplicates marked?  I wasn't able to find any documentation about this.
> Does it ignore them or treat them as normal reads?
> >
> > Thanks,
> >
> > Fong
> > _______________________________________________
> > miso-users mailing list
> > miso-users at mit.edu
> > http://mailman.mit.edu/mailman/listinfo/miso-users
>
>
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