Three questions: 1) When specifying a reference genome, what are the advantages and disadvantages of using Hs38 vs Hs38 canonical? 2) On Bowtie2, under "select reference genome", my workflow says Hs38 (Homo sapiens), but cuts off before I can determine if it is set ot Hs38 or Hs38 canonical. Clicking on it gives the list of options without highlighting which one was selected, so I have no way of knowing, other than remembering what I think I selected, and hoping that by looking, I haven't changed the selection. Can this be modified? 3) What is the syntax to eliminate variant sites where the chance of a false positive call is greater than 1/10000? is it -f "QUAL > 40" in VCF filter, and is VCF filter or Naive Variant Caller the best tool to do this? I haven't yet stumbled on a place where quality syntax is explained.