Re: [Samtools-help] samtools calmd behavior and MD tag

[Martin M. <mmo...@gm...>]

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