Use bam files with MM and ML tags with native 5mC calls, no bisulfite conversion.

[faulk-lab]

metheor looks like exactly the tool I need, however I am not using bisulfite data as input. I called methylation directly using nanopore sequencing and my .bam files store it with MM and ML tags according to the new standard from the SAM working group. https://samtools.github.io/hts-specs/SAMtags.pdf

As direct methylation sequencing takes over from bisulfite based methods, metheor would be incredibly useful if it would take these bams as input. Can you please update the software for this enhancement?

Alternatively, how can I convert my bam files into pseudo bisulfite versions in the meantime?

[dohlee]

Thank you for your suggestion! Actually I'm not familiar with the convention of using MM/ML tags at the moment, so I'll take a deep look on it and get back to you.