Why are we using -B 3 (tumor mismatch penalty)?

[maxulysse]

We should have more information on why we're doing that. I do believe it's a good idea, but can we back it up? https://github.com/nf-core/sarek/blob/05c6e0b63251af83b9e7d5b259cec9e679fccf57/main.nf#L673-L681

[FriederikeHanssen]

Ok to keep the discussion, issue specific. I so far could not find another pipeline or pipeline supporting this. Actually the default mismatch penalty is 4:

Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. [4]

qith B being the mismatch penalty (4) and A being the matching score (1)