The response speed is awesome!
On github Eric answered:
https://github.com/galaxyproject/tools-iuc/blob/0887009a23d176b21536c9fd8a18c4fecc417d4f/tools/bedtools/multiCov.xml see L12 of that file for where the bai file is stored.
That explains a lot. Very precise example. Thank you!
What I'm still wondering is:
When is it being generated, what code is used for that?
More specific:
When I use Picard SortSam in galaxy, the output is a bam file with an accompanying bai file.
But when I use Picard on command line, the output is just a bam file.
In the Picard SortSam galaxy tool, it is not being done. (If I didn't miss something)
What leads me to
When I do multiple actions with my bam file - is the index generated every time? (overhead)
GATK processes BAM files and at the same time the bai files.
It would be a waste to just use the bam files and re-generate the bai files, that already exist.
How could that be done?
Thanks,
Alexander