I am a new user of bbmap. I am trying to align short reads to reference sequence of 1200 bases and I would like have NO penalty for the overhangs on either ends to my reference sequence, but otherwise normal penalties (for mismatch, etc) within the reference sequence. Are there specific parameters of bbmap that I can adjust in order to achieve this? Thank you.
Sorry, that's not quite possible. You can approximate it with the "local" flag, but reads will still prefer for example a 100bp perfect match over a 90bp match with a 10bp overhang.
In normal mode, BBMap does not penalize overhangs very much - about 30% as much as a mismatch. In "local" mode, overhang bases are not penalized at all in the final stage of alignment, but they are still penalized in the early stage of alignment. If you want the maximum number of the sequences to align (including sequences that are mostly overhang), add the flags "minid=0.5 local".
P.S. Strictly speaking, BBMap has no penalty for overhang, it's just that no points are awarded for overhang, either, whereas they are awarded for matches. In local mode, overhang bases are completely ignored in both the denominator and numerator.