Keiran Raine wrote: > >> On 2 Aug 2016, at 15:31, Martin MOKREJŠ <mmokr...@gmail.com >> <mailto: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
Hmm, but I do not see it in the manpage, not even in the "bwa mem" commandline output. Here is my commandline: bwa mem -t $threads -p -M -R "@RG\tID:$prefix\tPL:$platform\tLB:$library\tSM:$sample" "$reference" "$q" | samtools view -@ $xthreads -T "$reference" -Sb - > "$s".bam Martin ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
