[miso-users] MISO Handling of Marked Duplicates

[Yarden Katz]

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
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