Is there any way to avoid adding the PG tag while creating a SAM output from BWA ?

Question

[lakhujanivijay]

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.

Answer 1

[Devon Ryan]

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.

[ATpoint]

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.