BWA alternate-aware alignment with Parabrick

Hi, may I know if the bwa-mem alignment software can be made to be alternate contigs aware?
The topic is covered in GATK4 below
https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38

Regards
Solyris