Question: (Closed) How to edit flags in a BAM file?
gravatar for rmccloskey
4.6 years ago by
rmccloskey180 wrote:

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?

samtools bam • 2.3k views
ADD COMMENTlink written 4.6 years ago by rmccloskey180
gravatar for Pierre Lindenbaum
4.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

Hello rmcclosk.math!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


PS: Duplicate of "Tool to unmark duplicates"
ADD COMMENTlink written 4.6 years ago by Pierre Lindenbaum119k

Oops! Sorry, I did a bunch of searching but failed to find that answer. Thanks!

ADD REPLYlink written 4.6 years ago by rmccloskey180
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