I am planning a large alignment run on a non human species using a non alt aware reference.
I would like to determine which combination of BWA MEM "-M" and "-Y" options I should be using.
As far as I can tell "-M" used to be needed for the Picard compatibility as sometimes mentioned in the man page.

GATK 4 now recommends not to use "-M" for the human alt aware reference.
But they are now recommending "-Y" which seems to be a new option from around (0.7.12?)

A small recommendation in the README.md would be useful.