Apologies if this is a simplistic question, I am new to Galaxy.
I am working on a variant calling workflow for paired DNAseq reads, with BWA-MEM as my aligner. Since I have custom parameters, I would like to manually enter them into BWA-MEM through the "Select full list of options" category.
I was just wondering if there are any maximum values for scoring I should adhere to. For example, if I want an ungapped alignment, what's the highest penalty score I can assign to -O? In the bwa manual, there are values in square brackets behind each argument, but I'm not sure what they represent. The default settings?