Apologies if this is a simplistic question. I originally asked this in the Galaxy Biostars channel but there was no answer, so I thought I'd try my luck here.
I am working on a variant calling workflow for paired DNAseq reads, with BWA-MEM as my aligner. To achieve high confidence when aligning to a polyploid genome I would like to generate an un-gapped alignment.
I was just wondering if there are any maximum values for scoring I should adhere to. What's the highest penalty score I can assign to -O? In the bwa manual, there are values in square brackets behind the different parameters. In the case of -O, it says "-O INT Gap open penalty ". Does this mean the maximum penalty score I can assign is 11, or does this represent something else?