bwa settings used by MiSeq Reporter

[thiNGS]

I have performed a MiSeq 2x300 PE run using the enrichment workflow. I have performed deduplication on the FastQ files and now I want to perform alignment. I have read that if you let MiSeqReporter perform the secondary analysis it would use bwa to perform alignment. Do you know which settings are used by MiSeq rep? I don't find any detail on the manual and I was wondering how I can replicate that analysis workflow (I know, I could let the software do this but there are specific reasons why I odn't want to ) Any help or suggestion would be greatly appreciated!

[Brian Bushnell]

With a normal sam/bam file, one of the header lines starts with "@PG", and should list the entire command line used by the aligner. You can see the header with "samtools -H file.bam"