Hi Keiran, cool, does it run in multiple threads? "samtools clamd" runs in a single thread in my hands, so this would certainly be a reason to change my pipeline.
Keiran Raine wrote: > Hi James, Martin, > > As James indicates BWA doesn't actually report the the correct MD tags as it > changes all ambiguity and N positions to ACGT (by some reproducible method). > > I had requested addition of functionality to biobambam(2) to recalculate the > MD if the read spanned any ambiguity/N positions: > > bamsort -h > This is biobambam2 version 2.0.50. > biobambam2 is distributed under version 3 of the GNU General Public License. > ... > calmdnm=<[0]> : calculate MD and NM aux fields (for > coordinate sorted output only) > calmdnmreference=<[]> : reference for calculating MD and NM aux > fields (calmdnm=1 only) > calmdnmrecompindetonly=<[0]> : only recalculate MD and NM in the presence of > indeterminate bases (calmdnm=1 only) > calmdnmwarnchange=<[0]> : warn when changing existing MD/NM fields > (calmdnm=1 only) > > This gives you control over the warnings if that's what you specifically care > about. Yes, otherwise I would just ignore them all. ;-) Martin ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
