I have encountered an issue where alignments have 0 MAPQ because of secondary alignments in alt contigs. This is usually fixed by bwa-postalt for regular DNA sequencing but it does not seem to work for bwa meth.

For example all alignments in chr1:155,252,932-155,257,513 have MAPQ of 0 with bwa meth but MAPQ60 with bwa mem.

Any thoughts?