BAM header surgery

wjeck

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Join Date: Mar 2009

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#1

BAM header surgery

03-12-2010, 12:27 PM

To follow up on another "how to" question, does anyone know of tools to get in and edit *.bam file headers? So for example if I want to fix some info about readgroups, sequence lengths or comments I can get in there and add/change them?

I've looked for such a tool, but did not find.
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drio

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Join Date: Oct 2008

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#2

03-12-2010, 08:05 PM

You want to use the picard tools (http://picard.sourceforge.net/).
Study carefully the examples and the documentation.

-drd
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wjeck

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#3

03-13-2010, 10:27 AM

Thanks! I was looking for ReplaceSamHeader, not included in the picard distribution I was working with.

It appears to work with unindexed BAM files as well as SAM.
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