bbmap for FAIRE-seq and other line than reference


I've read the post bbmap and chip, I'm sure that bbmap is ok also for other chromatin-level applications.
I'm trying to map some maize lines (DNA from FAIRE experiment) to reference line. So there are problem, that the aligner must cope with a number of indels, snp and so on.
I wonder, how could I allow bbmap for this variation. Now, setting mapq=10 filter in samtools I see, that my mapping percentage is only 15-30 ! The maize line in question is somehow different from the reference.

My current code is for i in {38..39}; do ~/bin/bbmap/ in=../reads_bbtrim/hds${i}_clean.fastq.gz ref=Zea_mays.B73_RefGen_v4.dna.toplevel.fa outm=../bbmaped/vs${i}.bam vslow k=8 maxindel=20 ambig=random minratio=0.1 32bit showprogress=100000 -Xmx100g statsfile=../bbmaped/stats${i}vs covstats=../bbmaped/covstats${i}vs ; done

I thought, that very sensitive setting and some parameters from the cited post would be ok.
So there are two problems: 1. use bbmap for FAIRE-seq reads, 2. equalize settings for maize line not-very-similar to the reference maize line.





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