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

[Keiran R. <kr...@sa...>]

For BAM in/out yes:

inputthreads=<[1]>            : input helper threads (for inputformat=bam only, default: 1)
outputthreads=<[1]>           : output helper threads (for outputformat=bam only, default: 1)


Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr...@sa...
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

> On 2 Aug 2016, at 12:57, Martin MOKREJŠ <mmo...@gm...> wrote:
> 
> 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




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