Q: Removing duplicates with HMMRATAC

[tamuanand]

Hi @EvanTarbell and @taoliu

Question: Does one need to MARK duplicates so that HMMRATAC can remove duplicates OR does HMMRATAC remove them.

Please advise.

https://github.com/LiuLabUB/HMMRATAC/blob/master/HMMRATAC_Guide.md (last edit 19-Aug-2019)

It is possible to remove duplicates or low Mapping quality reads before 
inputting into HMMRATAC, although HMMRATAC will perform 
these functions by default. 
By default HMMRATAC will remove duplicate reads
(and this function is currently hard-coded and cannot be turned off)

#72 (comment) (answered 05-Oct-2020)

HMMRATAC removes reads that have been MARKED as duplicate.