is there a way to modify the default way Galaxy creates the index *.BAI files? We work with a large salamander genome, therefore, quite some coordinates in the BAM files are beyond 2^30. Therefore, the index files have to be created using either biobambam2:bamSort or samtools index -c -m 14. However, I cannot really figure out if there is a simple way to "teach" Galaxy how to do that. We have our own institute's Galaxy instance, therefore, I can change pretty much anything there...
I am sorry if a similar question was posted before and would be thankful for any advice.
Best regards, Sergej