> Il giorno 06 apr 2018, alle ore 14:54, James Bonfield <j...@sanger.ac.uk> ha > scritto: > > On Thu, Apr 05, 2018 at 01:02:30PM +0200, ernesto.picardi wrote: >> I'm using samtools calmd to add the MD tag to my bam file generated using >> minimap2. >> The added MD tags included lower case characters. Is this correct? According >> to SAM specifications, MD should contain only upper case characters >> MD:Z:[0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)* > > It's just reporting whatever is in the reference at this point, and if > the ref is lowercase then the MD string gets lowercase added to it. > > Given the spec states it is uppercase only this is probably a bug in > samtools.
Many thanks! Hope it can be fixed as soon as possible. In the meantime I’ll use the reference in upper-case. Best, Ernesto ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
