Question: Does CopywriteR consider reads marked as duplicate?

PeeperLab / CopywriteR

DNA copy number detection from off-target sequence data

GNU General Public License v3.0

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Closed messersc closed 6 years ago

messersc commented 6 years ago

Hi,

I have a question that I could not find an answer to reading the publication or the R package docs:

Does CopywriteR consider reads marked as duplicate? I suppose it does, but I want to make sure.

Thanks, Clemens

thomasKuilman commented 6 years ago

No, it does not. It looks for reads with high mapping quality (>37) and for 'proper pairs' in case of paired end sequencing.

Regards, Thomas