What is the correct way to map Hi-C data with bwa mem?
See here, in particular slide #10 from the tutorial:

bwa mem -5SPM ref.fa read1.fq read2.fq &gt; out.sam


Here, -SP disables pairing. The Aiden lab and this paper also use a similar command line. Beware that there are many Hi-C pipelines, but not many are using bwa-mem.