Hi, I'm wondering how to go about transforming a file between different bam formats. In particular, I am interested in switching a file mapped with BSMap into the Bismark bam file format for downstream analyses. I want to do so because BSMap, from simulations I've run, maps heterospecific reads with fewer biases, but Bismark has better tools for downstream analyses like looking at allele-specific methylation.

For the most part, this seems a simple case of switching the location of columns in the file. However, is there anything I'm overlooking about formatting these files and is ther anything that can be done about the flags that are reported for Bismark, but not BSMap?

Thanks in advance for the help or advice!