bismark score_min; CpG cytosine?

[mbk0asis]

Hello,

In my knowledge, one can change mapping stringency with the score_min option by adjusting mismatch/indel penalties.
What I'm curious is whether cytosines in CpG contexts are also counted as mismatches. If so, should I give more relaxed parameters than ordinary mapping such as bowtie?

Thank you!

[fkrueger]

The score_min function only adjusts the penalties for non-bisulfite mismatches. All positions involving Cs, irrespective of its methylation state, are treated as T and hence do not count towards the limit set by --score_min.