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

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

> On 2 Aug 2016, at 15:31, Martin MOKREJŠ <mmo...@gm...> 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>


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