negative filtering?

[alexlenail]

Does sambamba provide the option of filtering out regions, e.g. if I wanted to filter out all the chrM reads from my .bam file?

[lomereiter]

I've just added a bunch of new filters for convenience—your case can be handled now by
--filter "ref_name != 'chrM'"
For sorted & indexed files, however, supplying a BED file is more efficient (needs some manual work but will skip even reading most reads in the region).