Jens Leinenbach

@Kim: You can run minimap2 with this option: --MD output the MD tag And you can add the MD tags afterwards with the Picard tools: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.1.1/picard_sam_SetNmMdAndUqTags.php

@Kim: You can run minimap2 with this option: --MD output the MD tag

Here is the reason why minimap2 does not use cigar strings in the modern format: https://github.com/lh3/minimap2/issues/157#issuecomment-385035416 Quote: " I think X/= is the second biggest mistake in the SAM spec (the top one being the bit flag). It is against the principle of alignment, inflates file sizes and has little use in practice as it doesn't tell us what are the deleted and mismatching bases. Typically I wouldn't consider X/= at all. "