Removing multiple tags with squeeze

[Thomas Keane]

Hi - I'm using the latest version of 'bam' (1.0.11) to strip some extra tags that were added by GATK BQSR (BI, BD, and BQ). However, the squeeze command only seems to be removing the first tag given in the --rmTags command line option. My command is:

bam squeeze --in test.bam --out test.strip.bam --keepDups --rmTags BD:Z;BQ:Z;BI:Z

Do you also see this behaviour?

Thanks,

Thomas

[Mary Kate Wing]

Try:

bam squeeze --in test.bam --out test.strip.bam --keepDups --rmTags "BD:Z;BQ:Z;BI:Z"

-or-

bam squeeze --in test.bam --out test.strip.bam --keepDups --rmTags 'BD:Z;BQ:Z;BI:Z'

Unfortunately I made a poor choice of delimiter, ';', between the rmTags.  If you don't put the tags in quotes, the ';' will be treated as the end of the command.

When I recreated your command without the quotes, I got: 

BQ:Z: command not found

BI:Z: command not found

I will update the wiki documentation to be clear that multiple tags need quotes around them. 

I will also update the command-line help.

Additionally, in a future version, I think I will update the code to also allow ',' delimiters between the tags.  That way they shouldn't have to be in quotes.

Let me know if adding the quotes fixes your problem.

Sorry for the poor documentation on this and the poor choice of delimiter.

Mary Kate

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[Thomas Keane]

Ah, yes I should have spotted that too. Thank you!

Thomas

[Mary Kate Wing]

No problem.  Just let me know if you have any other questions or issues regarding bamUtils.

Mary Kate

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