Circle-Map tutorial not working with hg38, but does work with hg19

[eallen-bbi]

I've been unsuccessful trying to reproduce the tutorial results when using hg38, but it works fine if I go back to hg19. When I use hg38, all of the reads align with mapq = 0, because they multi-map both to the expected region on chr7, but also to some of the "fixed" chr7 contigs that are part of the hg38.p12 reference (e.g. chr7_KZ208912v1_fix). When I align to hg19, these fixed contigs are not present, and the results are as expected. The paper indicates that this version of hg38 reference was used, but do I need to filter or pre-process the reference or use bwa mem differently than is shown in the tutorial ? Thanks !