Question: Is there any way to avoid adding the PG tag while creating a SAM output from BWA ?
0
gravatar for lakhujanivijay
6 days ago by
lakhujanivijay4.6k
India
lakhujanivijay4.6k wrote:

Hi

Is there any way to avoid adding the PG tag while creating a SAM output from BWA ? The only option I could think of is to use samtools reheader and adding a new header without the PG tag. I am wondering if that would be possible during the mapping step itself.

bwa sam pg • 59 views
ADD COMMENTlink modified 6 days ago by Devon Ryan93k • written 6 days ago by lakhujanivijay4.6k
1
gravatar for Devon Ryan
6 days ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

You can pipe the output through grep and use grep -v @PG, but the question then becomes why you would actually want to do that. It's usually best to keep that information in there in case you need it down the line.

ADD COMMENTlink written 6 days ago by Devon Ryan93k

Yep, I also suggest to keep it in case you mislable the file accidentlly so this entry might help you figuring out what the file actually contains and how it was created.

ADD REPLYlink written 6 days ago by ATpoint26k
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