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

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
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updated by Devon Ryan Devon Ryan • written by lakhujanivijay lakhujanivijay

1 answer

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.

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written by Devon Ryan Devon Ryan

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.

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written by ATpoint ATpoint

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