[miso-users] MISO Handling of Marked Duplicates

[Fong Chun Chan]

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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