I have a number of BAM files with a very high number of reads flagged as duplicates (>50%). To confirm that these are indeed duplicates and the flags were not introduced erroneously during processing, I would like to clear all the duplicate read flags and run Picard tools MarkDuplicates to recheck these. Is there a better way to change the flags in a BAM file then to convert to SAM, edit the file with sed or something, and then convert back to BAM?
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Cheers!PS: Duplicate of "Tool to unmark duplicates"