Question: (Closed) How to edit flags in a BAM file?
1
gravatar for rmccloskey
4.6 years ago by
rmccloskey180
Canada
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
0
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.

Cheers!

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
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 986 users visited in the last hour