Hello, it's not clear to me if the multisample mode is actually a join calling, or if it's simply the equivalent of bcftools norm + bcftools merge. I am specifically interested in NOT doing join calling. I am also wondering if base recalibration is still necessary? I find tutorials where it's done, but the doc of callvariants doesn't say anything about it. I am aware quality recalibration in itself is not trivial and there are probably pros and cons in doing it.
Sorry the questions are rather general, I hope it's acceptable. I know some people here use bbtools, so I hope to get an answer.
Thanks for any feedback you could give me.