I have been using Rsubread to map reads to a short reference sequence (amplicon sequencing). The output CIGARs are in the M format rather than the X/= format. Is it possible to get Rsubread to report mismatches with X?

Thank you!

Looks like this:

> cigarbam.ms)
   [1] "239M11S"     "250M"        "250M"        "250M"        "250M"        "250M"        "250M"

I would prefer this:

> cigar(bam.pb[1:10])
 [1] "162=1X36=1X77=2X206=1X745=3X103=1X266=30X112=" "324=1X1279=30X112="                           
 [3] "125=1X17=1X822=1X637=30X110=3S"                "1740S200=1X394=1X1008=30X108=3S"   

Rsubread uses the M format. You can however get the number of mismatches from the NM ("edit distance") tag: the number of Xs is NM minus any insertions or deletions.

This is something we will consider in the future development. But it is not supported at the moment.