Does GATK honor the SO BAM header tag?
This is not specifically answered in the Collected FAQs about BAM files so need a confirmation.
Do all GATK tools use the SO tag in the header to indicate if the BAM file is sorted? In other words, if the input BAM to a tool is sorted, but the output is not, would GATK alter the SO tag?
As an example, does IndelRealigner produce a sorted BAM?
The SO tag of the ouptput says SO:coordinate, but my input was also sorted. I'd like to assume that all is well, but would like a human confirmation.