BAM header surgery

[wjeck]

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.

[drio]

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

[wjeck]

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.