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. James -- James Bonfield (j...@sanger.ac.uk) The Sanger Institute, Hinxton, Cambs, CB10 1SA -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ 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
