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Question: Is there any way to avoid adding the PG tag while creating a SAM output from BWA ?
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gravatar for lakhujanivijay
9 months ago by
lakhujanivijay ♦ 5.2k
India
lakhujanivijay ♦ 5.2k 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 • 197 views
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modified 9 months ago by Devon Ryan ♦ 96k • written 9 months ago by lakhujanivijay ♦ 5.2k
1
gravatar for Devon Ryan
9 months ago by
Devon Ryan ♦ 96k
Freiburg, Germany
Devon Ryan ♦ 96k 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 COMMENT • link written 9 months ago by Devon Ryan ♦ 96k

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 REPLY • link written 9 months ago by ATpoint ♦ 38k
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