> On 2 Aug 2016, at 15:31, Martin MOKREJŠ <mmokr...@gmail.com> wrote: > > "samtools calmd" is the first tool in my pipeline writing out the MD: tag, > but as it turned out this is more about NM: tag being mistaken, and that > was bwa mem's job. (I don't even know how to tell bwa mem to output also MD: > tag at the first sweep.
MD is automatically generated in BWA mem since 0.7.6: https://github.com/lh3/bwa/blob/master/NEWS.md#release-076-31-januaray-2014 <https://github.com/lh3/bwa/blob/master/NEWS.md#release-076-31-januaray-2014> > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust 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.
------------------------------------------------------------------------------
_______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
