when I 'produce' a bam file in my output, I can download the bam file and a
corresponding bai file.

I am now wondering where does the bai file come from?
When is it being generated, what code is used for that?
When I do multiple actions with my bam file - is the index generated every
time? (overhead)
Where is the bai saved on disk (if it is)?

I found that in the IUC gatk, a new bai is always generated when a gatk
tool is started. This creates quite an overhead. Isn't there a better

@ref https://github.com/galaxyproject/tools-iuc/issues/194

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