Unsorted BAM output for bwa mem?

[dpryan79]

We have a HiC-related tool that's available in Galaxy that requires SAM/BAM input that is not coordinate sorted. As input, we normally use BAM files produced by bwa mem, which work well except for the fact that one needs to undo the coordinate sorting. Would people be open to me making a PR that adds a "do not sort the output BAM file" option? I would propose to hide this under a conditional (as is done with all of the "analysis_type" stuff currently) and have it default to "No", so people are less likely to accidentally select it.

This would save people time and disk space when doing this sort of analysis.

[mvdbeek]

I would support this, but we should perhaps also introduce an unsorted BAM datatype for this purpose.

[dpryan79]

I think the new datatype ship has already sailed, though that would be a nice orthogonal change.