If a BAM file is sorted then it can be opened in WD with samtools based DBI (because index could be built only for sorted BAMs).
But if it is unsorted, then it just can be imported to ugenedb. And it is very slow.
For example, times for 100 Mb unsorted BAM:
1) import to ugenedb = 2 h 30 min.
2) sort using samtools = 29 sec!!!
3) build index for sorted one using samtools = 2 sec.
4) import sorted one without index = 13 min 20 sec!!!
5) import sorted one with index = 1 min 34 sec!!!
So, it is better to sort a BAM file using samtools and then use the sorted one in WD.